VMware have finally released a patch to fix the Major CBT bug that causes your backups to be corrupted because the changed blocks are reported incorrectly.
Within the release notes for the 5.5 latest patch, its kind of hidden away to the point that I missed it the first time.
When you use backup software that uses the Virtual Disk Development Kit (VDDK) API call QueryChangedDiskAreas(), the list of allocated disk sectors returned might be incorrect and incremental backups might appear to be corrupt or missing. A message similar to the following is written to vmware.log: DISKLIB-CTK: Resized change tracking block size from XXX to YYY For more information, see KB 2090639.
You can get the patches below for your version of choice, however there is no fix for ESXi 4.x yet.
ESXi 5.0 Patch 10 – Patch information
ESXi 5.1 Update 3 – Patch Information
ESXi 5.5 Patch 4 – Patch Information
You will need your my.vmware.com login details to access the patch repository to download the zip file, then just import it into your VMware Update Manager within Admin View.