Eclipse seems to not be uptodate at all times with the filesystem in those dialogs...
E certainly has plenty of annoying bugs, however I've never seen anything on the scale of badness as being out of synch with the FS, so I'm almost certain that's not true. Unless you are running a beta, in which case ... well, you're on your own. Officialy you aren't supposed to use such things for "real" code, so...
I made my own manifest.mf, and used export... but still have problems, it can't find the external classpaths I'm using...
manifest.mf:
Manifest-Version: 1.0
Classpath: ./libraries/gagetimer/timer.jar ./libraries/lwjgl/lwjgl.jar
Um, read the docs

? It's "Class-Path:".
Doesn't matter, but you don't need the leading "./" and long experience with Sun's JVM's suggest it's a bad idea - sometimes their code won't work if you include a "./" (although maybe all those bugs have now been fixed, I wouldn't bother risking it).
I suppose I also need a library parameter for the java VM (-D) to ue lwjgl and gagetimer...
is there a way to include that in the manifest?
This is better covered in LWJGL's instructions I believe; off the top of my head you usually need the -Djava.library.path=. option on linux because of IIRC bugs in sun's loading of libraries under linux, but not for any other OS (whose JVM's do things properly when loading nativelibs). If you launch it via webstart, all will be fine.