Is keeping the file within the structure of the rest of the data important or can you move it outside of the scope of the zipped folder and have an uncompressed folder named PartofBigBag then place this folder + zipped folder within a folder such as OldData then the zip process should be fine and you have most of your data compressed.
I havent run into this specific issue but did have once an issue with defrag puking on not wanting to defragment a hard drive with 15% free and large video game installation files that were acting like a defrag roadblock. My solution was to move the files that defrag puked on working around to a different drive, defragging the drive and then repopulating the drive with the files that defrag puked on with XP.
Apples to Oranges since your dealing with Zipping (compression) and I was dealing with Defragmentation, but somes it can be picky and creative work arounds are needed.
Getting back to zipping I have also run into path being too long to compress before as well, solution with that was to shorten the path to compress.