I would guess that copying to RAM without problems and not to the hard drive would be a buffer issue with the serial port controller and hard disk drive not able to hold the incoming data until a disk write occurs; however with the limitations you have, just continue to write to RAM. Tracing down the software problem is likely to be a pain and upgrading the hardware expensive (well to some folks). But there are better add on boards with serial devices better designed/made and hardware for storage solutions that are more scalable.
