Hi Jim, I realise it's quite a while since this post was created .
I haven't noticed this with PDM 2016, I can click on a file and it remains highlighted until I click somewhere else. Do you have a screenshot or video you could post?
I finally figured out the cause of this problem today. In the EPDM options window is the following option:
On my machine, it was set to 'Always' and that is when the problem would occur. If I set it to 'Prompt' and then select my model in the EPDM tree, the following appears:
Selecting 'Yes' will cause the problem behavior (the file becomes unselected), selecting 'No' will not cause the problem. Setting the option to 'Never' seems to fix the problem entirely. I found SPR 609139 which seems to describe the same issue.