I did read that, and i think i need to tackle the windows issue first.. either that or the rear boot isnt locked even though the switches say it is.
also came across this
Troubleshooting Failed Initializations
- Check battery voltage: Low system voltage prevents the JBE from completing module routines. Ensure your battery is fully charged or jumped. [1]
- Inspect the hardtop/convertible top status: On the E89 Z4, the JBE shares signals with the Convertible Top Module (CTM). If the roof is unlatched or stuck in a microswitch fault state, windows may lock out.
So yeah ill have a look once i fix the battery, thats prob step one. or not.. lol who knows.. but thats prob a good point to start first at. 
Chippie, thanks for the link mate, but i cant access that pdf for some reason, but i did rear the webby version of it, before he made a pdf of it.
also just spit balling some ideas ill try when i get home..
Sometimes the top is physically closed but hasn't compressed the microswitches fully. [
1,
2]
- Ensure the luggage compartment/trunk partition is firmly locked into its lower position.
- Insert your physical key into the driver's door lock cylinder.
- Turn the key to the Lock position (left) and hold it continuously for 20 to 30 seconds. This signals the CTM to run an emergency closure cycle and can force the roof hooks to fully clamp shut.
- Turn the key to the Unlock position (right) and hold it for 20 seconds to see if the windows drop. [1, 2]
(which is one of the reasons that the windows are locked out)
e89 jbe can't initialize windows
To fix a
BMW E89 window initialization failure controlled by the Junction Box Electronics (JBE/JBBF), turn the ignition on without starting the engine. Press and hold the window switch down until fully open, hold for 15–20 seconds, then pull the switch up until fully closed and hold for another 15–20 seconds. [
1,
2]
Manual Reset Steps
- Turn ignition on: Press the start button without putting your foot on the brake.
- Lower the glass: Press and hold the window switch down until the window is all the way open.
- Hold at bottom: Keep holding the switch down for 15 to 20 seconds to reset the limit and pinch protection.
- Raise the glass: Pull the switch up to the second click position until the window is fully closed.
- Hold at top: Keep holding the switch up for 15 to 20 seconds. [1, 2, 3, 4]
Troubleshooting Failed Initializations
- Check battery voltage: Low system voltage prevents the JBE from completing module routines. Ensure your battery is fully charged or jumped. [1]
- Inspect the hardtop/convertible top status: On the E89 Z4, the JBE shares signals with the Convertible Top Module (CTM). If the roof is unlatched or stuck in a microswitch fault state, windows may lock out. [1, 2]
- Use a diagnostic tool: If manual holding fails, use a BMW-specific tool like ProTool or BimmerGeobs/Standard Tools to clear JBE fault codes and run the active "initialize windows" service function.
all windows and yes warning lights on the roof button
The warning lights on your roof button mean your
window initialization failure is a symptom of a convertible top fault, not a broken window system. [
1,
2]
On the BMW E89, the Junction Box Electronics (JBE) and the Convertible Top Module (CTM) communicate directly. As a safety feature, if the car cannot verify that the hardtop is 100% closed, locked, and secure, the CTM instructs the JBE to
lock out and disable window functions to prevent the roof mechanisms from striking and breaking the glass. [
1,
2,
3]
You will not be able to initialize or properly operate the windows until the roof fault is addressed. [
1,
2]
Immediate Steps to Resolve the Lockout
1. Try a Manual Roof Mechanical Reset
Sometimes the top is physically closed but hasn't compressed the microswitches fully. [
1,
2]
- Ensure the luggage compartment/trunk partition is firmly locked into its lower position.
- Insert your physical key into the driver's door lock cylinder.
- Turn the key to the Lock position (left) and hold it continuously for 20 to 30 seconds. This signals the CTM to run an emergency closure cycle and can force the roof hooks to fully clamp shut.
- Turn the key to the Unlock position (right) and hold it for 20 seconds to see if the windows drop. [1, 2]
2. Identify the Flashing Light Pattern
The light on the convertible top button tells you where the system is stuck:
- Flashing Red: The roof movement is unlatched or interrupted (often a microswitch or wiring issue).
------
A
flashing red roof button when the hardtop is physically closed means the Convertible Top Module (CTM) did not receive a final confirmation signal from the microswitches to prove the roof is fully locked shut. Because the CTM thinks the roof cycle is still running or incomplete, it is actively locking out the Junction Box Electronics (JBE), making it impossible to initialize or roll your windows up or down. [
1,
2,
3]
You must satisfy the CTM's locking sequence before the window system will unlock.
and
Step-by-Step Triage for a Closed Roof with Flashing Red Light
1. Perform a Hard Battery Reset
The CTM can easily get caught in a software loop if a sensor signal drops momentarily.
- Turn the car completely off.
- Disconnect the negative battery cable in the trunk.
- Wait 15 to 20 minutes to completely drain the modules' capacitor memory.
- Reconnect the cable. Start the car, and immediately check if the flashing red light turns off or if you can now pull the windows up. [1]
2. Clear Obstructions and Cycle the Trunk Partition
The E89 is incredibly sensitive to the luggage compartment tray position. [
1]
- Open the trunk manually if needed.
- Unhook and reset the trunk partition multiple times to ensure it snaps cleanly into its lower position.
- Even though a bad partition switch usually triggers an amber or solid red light, a faulty or loose sensor sequence can cause permanent cycle failure, resulting in a flashing red error. [1, 2, 3]
3. Manually Compress the Cowl Hooks (If Slightly Unlatched)
If the hydraulic pump shut off milliseconds before the roof fully clenched into the front windshield cowl, the microswitch will register as open. [
1,
2]
- Sit in the car with the ignition on.
- Press and firmly hold the roof "Close" switch down for up to 60 seconds. Listen closely for any motor hum or mechanical clicking near the top of the windshield.
- If you have a helper, have them gently push down on the outer front edge of the roof shell from the outside while you hold the button to help the latches grab.
Ill run through these when i get home