@utri007That the Apollo accelerator is bugged upto its guts has been known for at least a decade. Specific timing fixes on some A1200 motherboards are required to make it work, then, as Thomas pointed out, memory not being added to the system in a proper manner, then failing on 3.9 BB2 rom update under some circumstances. Yes, they may work ok without any drama if you get exactly the right motherboard, and have a bit of luck running some apps.
That was one of the reasons Jens Schoenfeld critiziced so much its design when he bought the Apollo rights long ago (a adecade ago?). He said something along the lines that he wanted to buy them to bury that bad design forever. You may find his technical arguments against it if you look hard enough on the EAB forum.
Anyway, back to your issue: it seems that you are running a customized kickstart rom. I have been there, done that. It is a nightmare waiting to happen. About 75% of the hacked/patched rom modules out there have a small issue here and there. Not recommended for stability. Bugs are going to surface and you will probably end up blaming it on to something else, like bad psu, old caps, or another patch or system program you use.
The unmodified 3.1.4 kickstart rom is superior to any previous version of AmigaOS rom out there. Let me give you a very quick summary of the changes between AmigaOS 3.9 BB2 and 3.1.4 roms on an A1200:
AmigaOS 3.9 BoingBag 2
bootmenu 44.7 (25.2.2002)
console.device 44.8 (12.6.2001)
exec.library 45.20 (6.1.2002)
FileSystem.resource 45.10 (3.8.2001)
FileSystem 45.13 (3.8.2001)
ram-handler 44.23 (8.4.2001)
icon.library 45.1 (8.2.2001)
scsi.device 43.43 (16.1.2002)
shell 45.7 (13.01.2002)
workbench.library 45.127 (21.2.2001)
TOTAL = 10 modules changed.
Note: Despite these changes, many are widely known to be buggy like ram-handler still displaying 100% ram disk usage while being empty. Or the failed scsi.device that does not support large drives and had to be hacked by users to try to fix it, workbench.library that could have its fuel gauge meter overflowing and also its memory leaking abilities, etc. I could go on and on about each of those modules.
AmigaOS 3.1.4
exec.library exec 46.45 (18.9.2018)
utility.library utility 45.2 (15.1.2018)
FileSystem.resource filesysres 46.1 (13.8.2017)
battclock.resource battclock 45.1 (30.11.2017)
graphics.library graphics 45.27 (20.9.2018)
layers.library layers 45.30 (31.7.2018)
gameport.device gameport 45.2 (9.7.2018)
timer.device timer 45.1 (14.7.2018)
card.resource cardres 45.2 (11.5.2018)
keyboard.device keyboard 45.2 (9.7.2018)
input.device input 45.2 (9.7.2018)
ramdrive.device ramdrive 45.3 (14.7.2018)
trackdisk.device trackdisk 45.1 (14.7.2018)
scsi.device IDE_scsidisk 45.7 (16.5.2018)
console.device console 45.4 (9.7.2018)
mathieeesingbas.library mathieeesingbas 45.9 (16.7.2018)
syscheck syscheck 45.1 (11.2.2018)
bootmenu bootmenu 45.6 (5.8.2018)
filesystem fs 46.13 (23.9.2018)
audio.device audio 45.15 (20.9.2018)
mathffp.library mathffp 45.3 (6.1.2017)
icon.library icon.library 45.22 (24.9.2018)
workbench.library workbench.library 45.194 (23.9.2018)
shell shell 46.10 (12.9.2018)
ram-handler ram 45.5 (6.5.2018)
expansion.library expansion 45.4 (12.9.2018)
And then you have the optional module: intuition.library 45.10 (16.9.2018)
TOTAL 24 modules changed + 1 extra optional.
Note: Only one bug uncovered in Shell, that is already in beta testing phase to be released free of charge for 3.1.4 adopters. The fix won't require a new rom.
It is an easy choice regarding kickstarts. I admit there is some nice stuff to have from the disk based components of 3.9, like ReAction programs, media players and internet stuff, but if you are looking for a better core OS, 3.9 is a certainly a well disguised nightmare, and 3.1.4 undoubtly kicks its ass a hundred times.
So stay safe and use an unmodified rom. We have had many success reports of 3.1.4 users
with Apollo accelerators. You should not be an exception.