We had the same issue that user was prompted to enter credential for each company some time ago and I believe it was coz User's TS profile was getting recreated everytime they logged in through RDP. Once we fixed user profile issue, issue resolved. So, check profile folder and see if there are some kind of permission issues Or for same problem as ours. Also, try it in different machine were it would create profile freshly and see if the problem occurs. For user security, did you look at Windows Authentication option...
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