Unfortunately I have not been able to reproduce this here. I have just tried again and, with the mainloop timer running in mIRC, edited and saved the file with the mainloop alias in mSLDev forty or fifty times without any issues being reported in mIRC.

If you test this in a clean copy of mIRC, installed a new, empty folder, with no other aliases/scripts loaded, do you see the same issue?

Are you using anti-virus software? If so, which type? If you disable it, do you see the same issue?