Still running the ST on the PC PSU through molex and it's working fine
I managed to find a clue on the monitor issue, when i go into the config menu of maxYMiser (music tracker) and set the "VB Freq" from low to high, the very same thing happens as when booting up to TOS with the monitor on before starting the ST, or going into the disk op menu in maxYMiser. That is, the picture is offset to the left about 1/3 screen, the brightness/contrast is lowered and not vertically uniform, and the colors gets scrambled, Restarting the monitor solves it as usual, and setting it from high to low doesn't cause any problem. The maxYMiser documentation doesn't really say what the option does more than that it might give a better picture (it does seem to give a slight better picture on "high"), so i'm unsure about what "VB" stands for. But it causes the very same thing as when restarting/starting the ST before starting the monitor. Also, when going into the disk op menu to load instrument etc, i get the same issue whether maxYMiser VB Freq is set to low or high... While a restart does solve it, it starts to get a bit annnoying as i'm doing quite some disk op:s which means constant monitor restarts

Have anyone got an idea for an easy fix for this, software-wise? Something like using another program to load stuff into maxYMiser than the TOS menu, or making some kind of setting in TOS?

Hardware ideas are appriciated too of course!
EDIT: Maybe i should mention that i have to wait for about a second after turning the monitor off before turning it on again, otherwise the issue remains. Also i found out that "VB" apparently stands for "Vertical Blanking". It seems to be related to some sort of refresh-frequency, i'm mostly clueless about these things

Getting a new monitor of some kind would be the easy way out, but this one does work fine apart from that need for restarting it at those times and i like having a real Atari monitor on top of my MegaST2/Megafile20-stack

Getting in touch with someone who knows a lot about CRT monitors would be great!
EDIT2: The MEGA ST2 and MEGAFILE20 errors have been solved! Now it's only the monitor left, this video illustrates the current problem that i'm having: http://www.youtube.com/watch?v=r3LNwIDcr4A
I've managed to isolate some specific operation that causes the monitor to go into this state. It never happens randomly and always happens when doing those specific operations:
* When powering on the monitor before the computer. The monitor then goes blank black and when the OS is loaded it gives this blue offset buggy image, which calls for a restart. If i power on the monitor just a second after the computer, it goes blank white instead and loads into TOS just fine.
* When going into a program (the one in the video, maxYMiser), and through the config of that program switching the Vertical Blanking Frequency from low to high. However, switching from high to low doesn't cause the problem. Puzzlingly, the file-selector dialog (part of the OS) that pops up when doing said disk operations always causes this error whether the VB Freq in the program is set to low or high, and whether the OS resolution (and thus also the file-selector dialog) is set to the same as the program (low, 320x200) or medium (640x200). Switching resolutions back and forth in the OS works without any issues!
* When jumping in and/or out of certain programs. Some cause it on start and quit, other just on quit, other just on start, other programs doesn't cause the error at all. For example, Everest works fine on both startup and exit. The maxYMiser 2006 Online Compo program works fine on startup, but when quitting it it causes the error.