Hi, I have this issue too. Here is more information:

In my case it's not files over 2 GBs in size that cause the problem. I only today noticed for the first time FileAlyzer giving wrong SHA-1 checksum for a file. The file is ubcd501.iso from http://www.ultimatebootcd.com/download.html and it is 291 MB in size. According to the web site, the SHA-1 is supposed to be 76d87e5f494aeda12d697c9ae62f24eec6eac3ef and other tools like Total Commander and Microsofts Sigcheck give this same SHA-1 checksum when I run them on my comp. But FileAlyzer gives wrong sum, 7FA46F3BB8DA46CC4C43353089584E71CA0E1B03. I don't think this is an issue on my computer, since other programs report correct checksum, must be a FileAlyzer bug. You can download UBCD and check checksums with FileAlyzer and I think you will see FileAlyzer for some reason counts them wrong.

Thank you anyway for this great tool, I use FileAlyzer lots every day and this is the first bug I have seen.