it has more to do with how you arrest a ped.
do you use the default lspdfr arrest by pressing and holding (e) or do you use the STP menu to arrest the ped(or any other plugin that takes over).
using the default arrest works if you transport the prisoner yourself or have the prisoner transported.
with transport, again you should use the default backup menu to ask for transport (B) if you use smartradio and you have Ultimate backup installed it will again use a different system i think(still need to test) but using the (B) menu to call for transport works like a charm.
so only the default LSPDFR arrest, frisking, transport etc. is synced to your profile.
if you have Stoptheped installed make sure you open the .ini file and set takeoverallarrests=no
when you get to the point you want to arrest the ped just don't click "arrest ped" but instead press and hold (e) to arrest after which you can do another frisk by holding (Q)
when you call for transport with (B) make sure you put the ped on it's knees by pressing (Q)otherwise transport is not available.
for alcohol and drugtest when already arrested, I use traffic policer keys (Lshift+O for alcohol / Lcontrol+O for drugtest) otherwise if not arrested I use the STP menu as I feel it is more user friendly.
hope this helps.