I have always used a .p12 generated off my imac on the PC. I downloaded openSSL and made my own .p12 on the PC as well (what a pain) but I see no reason to go through that when keychain will create it for you in 2 seconds. Request cert, send to ios provision portal, receive *.cer, install in keychain access, export .p12, copy to PC. No issue at all.
I myself choose a PC as I need faster hardware. I see no reason you need to leave your preferred development environment for provisioning or certificates.
Any more specific info? I don't even have any Adobe software on the iMac, I just use it for XCode and outputting .p12 files essentially. I assure you Flash Pro CS5.5 and Flash Builder 4.6 accept the p12 file generated from the mac without any issue. You should not be recreating anything at all between environments.
If you get any specific error feel free to post it here. Chances are it will be an issue with something else.
One thought is, as you nuke/regen your certificate you don't automatically assign your provisioning back to that certificate. So you'd need to go into each provision and select the newly generated certificate. When you look at your certificate and roll down what profiles are applied to it you need to make sure your app is properly applied to it. As long as it is you can generate the p12 from that.
If you add a new project, you NEED to make sure you select that certificate as you provision your new app and then simply re-download the certificate and generate a new p12 to make sure that p12 has the new app in it.
For a company that claims simplificty is their fortey, apple made their whole provisioning system insanely complex for new users.
I went back and removed all my past certificates and profiles and started all over again.
After a couple of wrong turns, I have had success, so thank you for your advice and encouragement.
I never did manage to findo out why my iPad would decide to not install my apps - it would have made life easier.
I think now I have the hang of the process and scarily understand it, while before it all seemed to be like some magic incantation.
One of the things I didn't grasp was that if you have a Mac, p12 generation on a PC is totally pointless.