You could be hit by a situation that I was hit by.
Does your application use any classes from the extension library (either the openNTF version or the IBM version - Update Pack 1)?
If so, the problem could be caused by not having the extension library installed on all computers that open the design in Domino Designer. I had this issue and found that just opening the design "touched" the Java classes (i.e. compiled them or at least signed them). This was due to the default setting in Domino Designer under "Project" to "Build automatically". So just opening Domino Designer from another computer without the extension library to adjust e.g. a form or @-formula agent, the Java classes were broken!!
It took us a little while to find out exactly why this happened. By disabling the "Build automatically" option we could avoid harming the code just by opening the database in Designer. However, a better approach is to install the extension library on all Domino Designer clients.
But be carefull since this issue can still harm your application since the elements get signed by the last user opening the design... :-(
/John