The standard process is to use a windows system to create windows runtimes and a mac system to create mac runtimes. With care, you can even merge the two separate runtime folders into a single folder with one set of database files, but with both executable files--provided you use the same "bind key" when creating both runtimes.
It appears you have a problem on your parallels machine. Not owning such a device (nor a Mac), I'm not exactly sure where the issue lies...
When you attempt to create a runtime for the second OS, are you trying to use the runtime database file (will have a .USR extension unless you specify a different set of letters) or the original .fmp12 file? You should use the .fmp12 file, but the same bind key (and file extension) if you want to merge the two solution folders.
Parallels is software to run windows on a mac. It's the same machine. Filemaker will run on the Mac and run on Windows.
When I create the Windows runtime version, I used Filemaker in Windows 7 (Parallels). The Mac version I used FileMaker in OS X. I'm using the defaults. I add the original .fmp12 file, The runtime extension is the default extension (fmpur) and the Bind key is default. It does not create the file. The last test I just ran, it errored out saying out of disk space. I have over 200GB of free space. I created runtime on Windows 7 pc. I create runtime on this mac under windows 7 without problem until I create runtime for mac. As stated above had to reinstall filemaker under OSX to create runtime for Mac. Now doesn't work under parallels Windows 7. I don't want to have to have two computers or reinstall filemaker each time to make runtime files. I think FileMaker doesn't know which runtime files to use in creating the runtime. It seem to use the runtime files for the version (Windows/MAC) I use the first time (After install) to create a runtime file. End result I would like to use 1 computer, boot FileMaker for Mac make runtime file. Boot FileMaker for Window and make runtime file. Have one Folder "My Program Mac Runtime", Second Folder "My Program PC Runtime".
Thanks for your help. I did a repair install of FileMaker on the Windows 7. I was then able to create the runtime for windows and then I went back to osx and created a runtime. Hopefully its fixed. I have not went back to windows 7 and tried it again,. If I have more problems I will post, incase someone else has this problem.