Reading the logs from a view days ago, had me have a closer look at uTorrentPortable.
As is known, uTorrent can take quite a while to really finish after it got closed by the user.
So if the user restarts uTorrentPortable again within the time uTorrent is still closing, as expected the launcher handles it as a secondary-launch. But the launcher is missing a CheckRunning-loop after Execwait, so the initial launcher will finish as well. Depending on, if uTorrent is locally installed or not, it will use the settings in %AppData%, or will ask the user to install uTorrent !
Basically it can be solved by including the CheckRunning-loop :
ExecWait '"$PROGRAMDIRECTORY\$PROGRAMEXECUTABLE" $0' CheckRunning: Sleep 2000 FindProcDLL::FindProc "${DEFAULTEXE}" StrCmp $R0 "1" CheckRunning
[edit: And I wonder if there is a reason why there is no PA.c-splash included ?]