Here is what the problem was. This is what I received from Steinberg support and my response. As always Steinberg support is awesome :
When I do a audio export mixdown.my midi files are not getting
exported.This only happens with the 64 bit version and does not happen if I do a
realtime export.This seems to have just started happening. There have been no
changes made to the system…I am exporting as a Mp file.Also the midi files
sometimes start at the beginning then just drop off.
I assume all of the plugins are 32b so they can also run in 32b Cubase? It may
have something to do with the VST bridge which is what allows 32b plugins to
operate in 64b environment.
Have you installed anything called J Bridge on the system? Can you email me a
simple project with this problem? Or maybe just create a new project using the
Grand 3 that has this problem. This will also help tell if the problem is only
with old projects or new ones as well.
Actually I am using Jbridge. Since you brought that to my attention I have been using Music Labs Real Guitar 32 bit through jbridge with no problems. About 2 weeks ago they came out with an update for 64 bit. I just removed the 64 bit dll and went back to jbridge with the 32 bit version and the problem went away. Hard to believe 1 instrument can mess up all the rest. Music Lab has some work to do. I am sure I am not the only one with this problem. Sorry to have bothered you with their problem.
Hope this helps anyone else with this problem