Apparently, a allocation table fault is the source of the problem (not that I'm 100% sure if it at all, but one of the linux based repair tool I tried tells me that).
I did use NTSF compression
September 08, 2014, 03:56:04 pm - (Auto Merged - Double Posts are not allowed before 7 days.)
OK I now have a 100% working computer again, I put all the (somewhat dated) backups back so I can analyze what's going on again.
1) I just experienced the slowdown just as described with VBA and the placebo BIOS. By using VBA + real BIOS or the real hardware this is fixed. I have no idea why this happens. I knew about this problem before releasing the patch, and thought I fixed it but I didn't. This is not a problem since it's an emulation problem and not a hardware problem, so technically I have nothing to fix on this one, VBA authors does
2) There is clicks in the sounds, just as said above. They happen in VBA once you use the real BIOS, strangely they don't appear with the placebo BIOS (however, strange clicks appear instead). On real hardware the clicks are here, but they are much less noticeable
3) The intro patch europe with orchestra somehow don't work at all and have no effect on the ROM.
I'll not be able to fix 1) because it's VBA's fault, and I'll only be able to fix 2) if I get help about those clicks. However I'll definitely fix 3) and try to release a version with a working orchestral intro, assuming anyone cares anymore.