Conspicuous changes in the encrypted Truecrypt container

I have a backup of my important data in the cloud with a given size of several gigs. To prevent snooping the data is inside a TrueCrypt container and everything which will be transmitted is the TrueCrypt container (no hidden volume).

Because uploading several gigs with even a fast Internet connection is slow, I have split the container file into pieces of several MByte size. I wrote a script which compares the current container with an instance of the past container (The past container is stored on the local disk to speed up the process) and only the changed pieces are written out and finally transmitted to the cloud.

Works great so far. Changes occuring from backup to backup weekly are in the 5% range of the original file, so updating is no problem.

Now a short time ago I prepared the backup and was wondering why it takes so long. I was puzzled to see that the changes have increased from the normal 5% to 50% ! Alarmed, I mounted both volumes (old one and the current one) and made a file compare and could not see any reason for the increase.

I have no knowledge how exactly TrueCrypt lays out the data internally, but as a file system the simple explanation could be that some data is heavily fragmented and deletion/appending such data could cause such an effect.

But I am still uneasy, so

a) Is the simple explanation correct and it is normal that changing only small portions of data could cause changes affecting a much bigger portion of the data in the TrueCrypt container ?

b) If you think a) is not a sufficient reason and you find that it is strange behavior, how to continue ?