I have this problem as well sometimes and I think I've managed to locate the fix (for my case, at least). I'll start by describing my observation on the issue.
The first sign for me that something is off is if the fs2crew PA graphic button panel does not show up when you have your intercoms set up and click the far right 'PA' button in the VC. When this is the case, I know the FO is going to act drunk and/or dumb for the rest of the flight and I might as well restart. He will do his flows normally as far as I can see, but during the preflight checklist he will insist that window heat is off when it is indeed on and do the same for one or more items. During the before start cheklist he will insist that the CDU preflight is not done and the anti-col light is off, regardless of their state.
He will not start the engines because "we are not configured for that", so I start them myself. When both engines are started and stable I have to manually switch down to the next flow/checklist item ('TO flaps' in this case) and say "Flaps 5". He will then report "Takeoff flaps set" but he will not start his B.taxi flow so I have to switch generators, set the aircon, turn on pitot heat/anti-ice and turn off the APU myself. He will then move on normally to the B.taxi checklist and that one has worked fine for me so far. Fast forward to the takeoff roll with everything working fine in between, he calls both V1 and Vr way too early and the fs2crew panel switches to "initial climb" while I still might have 10-40kts to go for Vr with a heavy load.
His after takeoff and 10k climb/desc flows are all good, same with checklists. The only hitch while in the air is that I can't use him to set anything on the MCP as he will, by magic, start the value at 0 and go infinitely upwards. Which means that using him to increase altitude altitude from TL 7000ft to 21000ft during initial climb results in the plane snapping down to level off while vnav disconnects. His adjustments of flaps, radio freq. and gear up/down are all good.
What works for me:
After a lot of problem free flights recently, until today, I am pretty convinced that loading the fs2crew panel (which intializes voice recognition) BEFORE switching to the 3D cockpit prevents the problem I'm having. I read this in another thread here a while ago which I think is buried by now. Test it by seeing if the VC 'PA' button actually brings up the fs2crew PA panel. That's how it seemingly works for me anyway. I uninstalled the old fs2crew before reinstalling the SP1c for 8-900 and 6-700 before installing the new fs2crew SP1 the day it was released.
I hope this helps at least some other experiencing similar issues. I use exclusively the B738 out of the NGX models because of my virtual airline and the problem does not seem to be related with airport, time of day or any other factors, but I'll pay extra attention the next few flights to confirm what I've just written. I use EZdok (I load the flight with EZdok off and start EZdok after fs2crew is loaded to get into the VC) and GSX and a registered copy of FSUIPC 4.81. I can also confirm that "EnableDataBroadcast=1" is present in the .ini-file.
-Steffen M