Huh, that's really weird. Are you launching straight from launchff7.exe, or are you using some other application or something to run this, such as Steam to launch it?
If anybody's familiar with AutoIt, here's the script for the current launcher; I don't think there's any glaring problems, but there might be. As I said before, it worked fine for me, but I'm going to rewrite it for AutoHotKey tonight and upload it, I'd like to know if it has the same problems.
If @OSArch = "X64" Then
$HKLM = "HKLM64"
If @OSArch = "X86" Then
$HKLM = "HKLM"
$musicdir = RegRead ($HKLM & "\SOFTWARE\FF7Music", "InstDir")
$ff7dir = RegRead("HKLM\SOFTWARE\Square Soft, Inc.\Final Fantasy VII", "AppPath")
Run (@ComSpec & " /c " & "start /min FF7Music.exe", $musicdir, @SW_HIDE)
Run ($ff7dir & "\ff7.exe")
while processexists ("ff7.exe")
edit: AutoHotKey is stupid and useless. It cannot properly read 64-bit mode registry keys when running as a 32-bit application, but if I made a 64-bit version then it would not run on 32-bit systems. Also, the language doesn't make a whole lot of sense, and the syntax is backwards, confusing, and inconsistent. Therefore, this solution is out of the question for now.