I had some issues installing Exchange 2010 SP1 Update Rollup 1 (KB2407028), and have had this same issue with other Exchange 2010 updates. I keep forgetting about this before installing updates. If you have defined an ExecutionPolicy for PowerShell, it screws up the update and gives an error 1603, even if you have selected to allow all scripts. See this link for the fix. Basically, just set the PowerShell ExecutionPolicy to “Not Configured”, force a Group Policy update, install the update, then put your original ExecutionPolicy back in place. Unfortunately, if the update attempts to install and is unsuccessful, you’re left with all of your Exchange services disabled. Once you successfully install the update, you need to go in and manually enable all of the Exchange services. PITA, but at least X is back up.
EDIT: After installing the update as described above, I discovered the next day that my OWA wasn’t working. I finally came across a forum post from a regarding a previous Exchange update that caused similar problems. The solution was to re-install the update from an elevated command prompt. I download the standalone installer for the update, right-clicked the icon for the command prompt and chose “Run As Administrator”, then dragged the update to the cmd window, which filled in the path and program info. Then hit enter, installed the update (which went smoothly), and tested everything and it FINALLY seemed to be working.
I don’t know for a fact, since I didn’t try it, but I have a sneaking suspicion that if your services were disabled by the original installation attempt, running the standalone update as an administrator, like described above, will probably fix them.