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It's not that Messenger Plus! is uninstalled everytime you restart your computer, it's just that it doesnt run/hook when needed. You should try the "alternate hooking" mode.
To do so, first run Messenger Plus!, so open your windows explorer and go to C:/Program Files/Messenger plus! 3 (or wherever you installed it
), and double click the msgplus.exe file.
Now close and reopen your contact list and the plus! menu should be there. Now go to Plus > preferences > miscellaneous. Under Messenger Plus! Automatic Recovery Options, set it to "Alternate". This should solve your problem
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