As @Microtribe already asked (in a different way):
How have you organized the data on the CF card? Putting too much files and subdirectories in a single directory is never a good idea and slows the file access down.
On modern computers this doesn’t really shows off, but on memory restricted, lower cpu power devices this slowdown can be dramatic and may even lead to crashes when not implemented carefully.
Another guess: have you unmounted/ejected the disk on the computer correctly after you copied the data? By just terminating the USB connection from the OT (or worse: only removing the cable physically) the data on the CF card may got corrupted (because the computer may not have finished writing the data to the card in the background). A corrupted filesystem (or the card gone bad) is the most likely reason for your problems.
I would at least perform some filesystem diagnostics on the card when you connect it next time to the computer …
And, no, in general 8GB is definitely not too much for the OT. Actually I have around 30 GB on my CF card (structured in many project folders and even subfolders) and I haven’t experienced any slowdowns or crashes.