Windows Installer version number fields have the following limits, set by Microsoft.
First Field - 0-255
Second Field - 0-255
Third Field - 0-65535
Fourth Field 0-65535 (Fourth field not checked in Product Version property but available in file properties)
You must certainly be creating very unstable software if you are running up against the 65535 limit on the third field, let alone the combined limit of another 256 x256 from the first two fields. Even Windows 7 beta is still under well under 10000 for the build number....