I got my motherboard and RAM stick replaced last week with identical parts. The happiest part is that it finally works without any problems! I got XP installed successfully then I formatted it and got my Debian installed.
After that I was able to correct my FSs using fsck (I couldn't correct that with the old system) and I haven't gotten any FS inconsistencies. I don't get any md5sum or sha512sum variations even with large files.
To conclude, my problems are gone. Appearantly the corruption was caused by the hardware issues. Several days ago I added an additional fan to be on the safer side in the future
I hope the problem won't happen any more.