I use FS Commander as well. One of the quirks of the programme is that if a waypoint VOR coincides with an intersection, FS Commander considers the waypoints to be
intersections, not VORs. If you look at the pln file you will see they are designated as I rather than V.
waypoint.0=, KCLE, , KCLE, A, N41* 24.53', W081* 51.09', +000791.00,
waypoint.1=KK, APE, , APE, I, N40* 09.06', W082* 35.29', +000000.00,
waypoint.2=KK, HVQ, , HVQ, I, N38* 20.98', W081* 46.19', +000000.00,
waypoint.3=KK, HMV, , HMV, I, N36* 26.22', W082* 07.77', +000000.00,
waypoint.4=KK, GIBSS, , GIBSS, I, N35* 59.71', W081* 50.31', +000000.00,
waypoint.5=KK, SPWAY, , SPWAY, I, N35* 49.10', W081* 43.39', +000000.00,
waypoint.6=KK, SHINE, , SHINE, I, N35* 36.52', W081* 35.22', +000000.00,
waypoint.7=, KCLT, , KCLT, A, N35* 12.84', W080* 56.58', +000745.00,
In the above pln, APE, HVQ, and HMV are VORs but the "I" after the waypoint designator means FS Commander has used the intersection, not the VOR. PF3 will therefore not allow a hold there.
Two ways around this. You can force FS Commander to use the VOR rather than the intersection (tedious), or you can manually change the "I" to "V" in the pln file and re-save it. Once the "V" is present, PF3 will allow a hold at the VOR. Sorry for the trouble but it's an issue with the flight planner.