I'm not exactly as knowledgable with the tech stuff as some of the guys around here are, but I can try to help. Firstly, when you say that 'everything' works fine, what types of programs have you tried? In my experience, despite the age of CS, it seems to be a memory pig, especially compared with other HL mods. If this error doesn't happen in any other program, you can try running CS like so:
hl.exe -game cstrike -console -heapsize <Amount>
wher <amount> is the memory in KILOBYTES, not megabytes, that Half-Life will use. Perhaps putting this to a relatively low number *may* fix your problem, and anything over 128MB and CS will still run fine. Ordinarily HL manages its own ram, but perhaps it's doing something wrong... just a thought.
I doubt this CS problem has anything to do with you not being able to format your HDD as NTFS, and on that NTFS problem I really can't help you... but I have changed my old Quantum drive from Fat32 to NTFS and back without changing any jumpers or BIOS settings.
I hope this helps... being an online HL player myself I know how you must feel 🙂