I don't think it has anything to do with OS/2.
If you can see only 638 KB of conventional memory, the reason is usually the BIOS - or a BIOS extension on some controller card - using the 2 KB as its data area.
Sometimes it may be possible to reclaim that area:
- if there's "Scratch RAM Option" in BIOS, try setting it to "0:300", rather than "DOS 1 KB"
- try to disable BIOS extensions if they aren't really necessary, or even completely remove cards like SCSI, RAID, etc.
Also, check everything with a good antivirus - it was pretty common for viruses to try to hide themselves by modifying the amount of conventional memory.
In 2003, I voted in favour of joining the European Union. However, due to recent developments - especially the restrictions on cash usage - I'm hereby withdrawing my support. DOWN WITH THE EU!