I have not seen this one problem listed and it may be a 1.0 target. Filed bug 3638.
Legacy installers modify autoexec.bat to add the install directory to the path and may also use set's. After the installer installs the program will not run as it's bin directory is not in the path. This also could be a reason why many applications only work when run from the directory it is installed in.
If windows type is set to 95 or less in winecfg then autoexec should be processed before running the program.
I also have programs which uses a pif to run a batch file. The batch in a pif is disabled/stubbed. I plan to look at filling it that feature when I get some time.
Paul Romanyszyn