I don't freeze / unfreeze my BFD3 tracks very often, but I don't recall having any issues when I did.
My system allows me to mostly keep BFD3 as an unfrozen midi track, to the end of the project.
I have never tweaked any of the settings in BFD3 preferences, have you ?
If you are short on RAM (as bitflipper suggests) another option within BFD3 preferences is to uncheck the "Enable BFD3 extended channels" button in the Streaming Engine section. Might be worth a try ? . . . though you're also saying other VST's do not freeze well on your system.
Perhaps you could post your system specs as a comparison to other BFD3 users within Sonar X3e.