I think you are suffering from the native behavior of MSP and the native behavior of Clarity. Once you integrate to Clarity with MSP, Clarity owns the schedule. Using certain features of MSP can create issues. For one, if you use % Complete in MSP it does a few things under the covers and updated fields in MSP. When imported to Clarity, fields are updated, and when exported back to MSP (prior to MSP 2010) certain fields are recalculated. In your case using '% Complete' in MSP might be the root cause of one of your issues.
Please see the attached picture as it shows how % complete in MSP can create milestones. You can prove it manually for the non-believers.
I am limited for time today, but basically there are certain features in MSP (prior to MSP 2010) that you should avoid using when using Clarity. Either that, or your PM's need to understand how MPS works and updates it's own fields in order to use % complete. I have another paper on this and am looking for it now.
So more information is on the way.