One problem I see is lines aren't being broken at 72 characters per the spec. For the compilation failures you're getting, does it look like it's missing definitions from one of the classpaths whose length is > 72 chars in the manifest?
My test projects with lots of class files have some entries that break this rule, but because they use some copies of the same jars in different places to pad out the number of classpath entries, it masks the problem so I didn't get any compilation errors.
Edit: actually, that doesn't seem to be the problem, playing with the paths more, the length doesn't seem to be a problem, or if it is, it's at a limit I (and your manifest) haven't reached. I think the 72 char limitation is for the MANIFEST.MF file that's actually packed in the jar file, and jar is more lenient and does conversions on manifests passed into it. But I haven't backed that up with a doc yet, it just seems to be the behavior.