I have encountered the same problem as many of you with multiple installations of Flight Simulator 9. See if any of this sounds familiar.
I have 3 installations:
FSGW3/(FS9.exe renamed to:) FSGW3.exe (Golden Wings 3 - Bill and Lynn Lyons)
FS2004/FS9.exe (my modern-day installation)
CA59/ (FS9.exe renamed to:) CA59.exe (The world reverted back to the CalClassic Era of flight - 1940s-60s [RadioRange-RDF days])
Now.... Autoinstallers will install to a root folder called "FS2004" because Micro$oft, once upon a time, had considered this for the name of the "Flight Simulator 9" folder and the coding is still in there.
The error your getting has to do with the fact that, if I understand it correctly, the registry entry for Flight Simulator no longer points to Flight Simulator 9/fs9.exe. That does NOT mean something is broken...only that your registry is pointing to another installation. (If you only have 1 installation, then something may be broken)
There is a registry repair tool for Flight Simulator that will repair your registry to point to 1 (and ONLY 1) installation of Flight Simulator. I don't use the modern day installation often, if at all anymore, so I didn't bother.
My personal fix was to install the A2A packages in to my modern installation (with the FS9.exe still named that) and everything went in, no problem. I then had to go back and hunt down all the gauge, effects and flightplan files by "date" and copy them to my other installations....where I wanted them in the first place.
I'm not complaining, mind you. I've been a fan for long time, and appreciate the need to protect the copyrights and attempts to prevent piracy via that "T" thingy, but if this installer is going to work like this, PLEASE put a list of the files that came with the package (along with the folder names that were put in the "aircraft" folder) so that those of us with mulitple installations don't have to spend up to an hour looking for all the effect and gauge files that were put in...Please?
Granted, this is just me, but I'm a paying customer, too.
P.S. Ok, 2 hours later, I have all the files re-found and copied to respective locations in my 3 installs. I have found one problem. Where are the gauges for the popup panel in the Ta-183? I have no Throttle lever or Elevator trim handles. ...and this brings me to the most pertinent point...Once I installed "Heavy Bombers and Jets", the patch posted at the beginning of this thread will NOT install in FS2004/fs9.exe...even though the package from the CD....DID! I can safely say that this little glitch isn't on me. Uhm...Help?
Just for clarification, this was a scratch installation, so no repaints or renaming of anything has been done after successful installation of "Heavy Bombers and Jets" v1.0. fs9.exe is in the folder. I did have one glitch in the installation of the base package, though. When the installer tried to contact ShockwaveProductions.net, and found no website there, it SHUT DOWN. Everthing seems to be there ..but a couple of Ta-183 gauges. Your installer for patch 1.1 will not install. I tells me my registry is corrupt, even though your own package just successfully installed...for the most part. Considering this is a patch, and (I assume) useless without the base package, would you please consider a manual or .zip folder that can run from the root FS (Flight Simulator 9) folder?
P.P.S. These planes look GREAT! I've had the B-17 for years as a seperate download, and now the P-51D-H and never had the issues I've encountered trying to install this patch. The P-51D-H patch went in just fine. Please take a second look at this issue.