I added the license file of my new BDS Ultimate to my existing license file.
The existing lic file had 42 x AutoCAD, 9 x Revit architecture suite and 6 x 3DS (in this order in the lic file)
With the new license placed at the bottom of the existing file, the Flexlm manager does no longer give out the AutoCAD licenses. after releasing the 9 Revit licenses (mainly to AutoCAD users) it returns an out of license massage to new users who try to start acad or Revit.
I am using FlexLM 11.4
Actual issue could be related this
http://usa.autodesk.com/getdoc/id=TS15255311
If all the licenses are available per the status, you could use the options file to control the license behaviour.
http://usa.autodesk.com/getdoc/id=TS1055247
also
Please update the license manager to 11.9
http://usa.autodesk.com/getdoc/id=DL16273699