1.5.2 Won't launch into alternate directory

I'm having a strange issue regarding the use of 1.5.2 and the "Game Directory" argument.

For some reason, it does not launch correctly into the alternate directory most of the time. However, it sometimes works as expected.

Attached is the log from the development console on the launcher. This was the launcher started with 1.5.2 uninstalled, then a profile launched with 1.5.2 selected.
The first run did not launch into the alternate directory, and launched into .minecraft. The second however did launch correctly. No modifications were made at all, it was simply a case of pressing play, quit, play, quit.
About 5 attempts were made to get this log, on one of them it launched correctly twice in a row, and on the other four it launched incorrectly twice in a row.

I've tried updating Java, changing the directory it's attempting to point to and various things like that, and I'm still left with this issue. This happens with both 64bit and 32bit versions of Java. It is also the case using java.exe over javaw.exe

Interestingly, debug.stitched_items.png and debug.stitched_terrain.png seem to launch into the alternate directory every time, but they are the only files that do this.