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Oh, sorry I just sent you a talk message before I saw your reply here.
Well the current build can't even write files larger than 2GB to ext partitions. I was also able to write a 4GB file to the same SD card and FAT partition (using the stock build or a PC) that this build could only write a 2GB file to, so it almost certainly isn't a filesystem issue.
Almost all FAT partitions nowadays are FAT32 (as older versions can't even make partitions that are larger than 4GB), so it is very unlikely that is the issue either.
It's been a while since I built linux, but it would seem that this is an issue with the kernel build. I would have assumed that large file support was always built in to recent kernels, but perhaps some how it was omitted or broken on this build?