I'm having the exact same issue since upgrading to 1.0.26. It seems the longer I leave the GMLive server running, the more times it reloads all my files when I start the game, sometimes it even times out entirely.
[47fe74c6|127.0.0.1:52198] ready! 16 live files, 0 globalvars, 55 macros, 228 scripts, 20 enums. Took 1361ms. [0c72fd6a|127.0.0.1:52622] ready! 24 live files, 0 globalvars, 55 macros, 342 scripts, 20 enums. Took 1815ms. [47fe74c6|127.0.0.1:52393] timed out. [0c72fd6a|127.0.0.1:52633] timed out. [054bf51f|127.0.0.1:52792] ready! 32 live files, 0 globalvars, 55 macros, 456 scripts, 20 enums. Took 5043ms.