L J,
I had this exact problem a couple weeks ago and spoke with NI support. I was running out of room when downloading my VI to the target. Remember that when you download a VI, you are downloading the top level VI along with all the subVIs contained in that top level VI (minus thier front panels). So the file you are downloading may be larger than you think.
Another problem that can happen every now and then is for the flash memory to become corrupt. Have you looked at your files over ftp? Have you noticed anything strange? If so, reformat your flash and you should be good to go.
As for your error log file, it is unlikely that the messages and errors you are seeing today are indicative of anything going wrong so long ago.
Hope this helps.