What version of Creo/ProE are you using (there have been several issues and fixes over various releases)? And could you describe the type of problem and parameters? Hard to tell what may be wrong without a little more information. It could be how you've set up the modal and dynamic frequency analyses as they are co-dependent. Here are some questions worth asking:
Are you requesting modes up to a frequency or a total number of modes? Also make sure to calculate Mass Participation Factors (assuming you are using base excitation since your model doesn't contain any loads) to help establish the "activity" of a given mode. Are you including all modes or just some (not recommended) and are you manually choosing the output interval or automatically? And what starting frequency and maximum frequency?
How long is your solution time and what form of convergence are you using? Are you using any mesh controls to avoid singularities? (I don't think this is the problem but always worth double checking)
Is your input log, semi-log, or linear? Make sure to double check your units, especially within your material definition.
Sorry for the onslaught of questions but I deal mostly with dynamic random and time analyses; however, I am sure some of the "quirkiness" of the inputs may be the same. My gut feel is that you are requesting your output accelerations/velocities/displacements with respect to ground instead of the supports. Stresses are not affected but the displacements will be. Just be sure whichever you select is what your after.
Good luck,
-J-