Hey there, folks!
So when I set up the new Papyrus build system, I *thought* I was ultimately making things easier on you guys, but it seems like it actually made it harder if you don't have a standardized Steam install.

BUT -- the new system was designed to be flexible above all else. It was made to deal with the lessons learned from working on DLC with its various script directories and so forth. So the good news is, you can still use it without having to go back to the nasty batch file which gets overwritten when we patch the game.
What you'll need to do: Make a file in your My Documents folder called "SublimePapyrus.ini". In that file, you'll need values for the scripts path, the compiler location, the output directory, and the flags file. Here is what it would look like if your Steam installation was in a standard spot on a Windows 7 machine:
[Skyrim]scripts=C:\Program Files (x86)\Steam\steamapps\common\skyrim\Data\Scripts\Sourcecompiler=C:\Program Files (x86)\Steam\steamapps\common\skyrim\Papyrus Compiler\PapyrusCompiler.exeoutput=C:\Program Files (x86)\Steam\steamapps\common\skyrim\Data\Scriptsworkspace=flags=TESV_Papyrus_Flags.flg
(Note you can probably leave the "workspace" value out since you're not using Perforce, but for the sake of completeness, there it is.)
So all you'd have to do is make those values point to the appropriate places on your machine, and the new build system will know where it's being compiled and do the right thing when you tell it to build.
The system tries to fill in these values by default so that most modders don't have to use the custom ini file, but I should have figured that all you clever folks would have tweaked setups with stuff in non-standard locations.

Let me know if this makes sense or doesn't make sense or still breaks or whatever.
Happy modding!
- Shane