I hate to do this to a cool Open Source product like MozBackup, but it really let me down the other day when I needed to transfer my email message base across from one machine to another. The backup file was fine, but contained only a small part of my data. Apparently the program can only cope with messagebases up to 4 GB in size. My messagebase is around 12 GB, hence the problem with only getting a portion of my messages in the archive file.
In the end I had to ditch MozB and go for the very excellent Static Thunderbird Backup which coped effortlessly with the 12 GB and moved everything over beautifully. Sorry Moz guys, but you really need to sort out that file size limit and fast. In this case $24.95 commercial beat out free OSS big time.