This issue pertains specifically to Minecraft, but it is affecting all Java programs that run on my computer.
It would seem that something is forcibly setting a _JAVA_OPTIONS environment variable. When I run my server, I have specified to allocate 4 GB of RAM to it with
-Xms4G -Xmx4G
in the startup batch file. However, when the server runs, It prints "Picked up _JAVA_OPTIONS: -Xms2048M -Xmx2048M" to the console, only allocating 2 GB. I have checked my system settings and there is no _JAVA_OPTIONS environment variable in the list. I do not want to add one, since that will also try to allocate 4 GB to Minecraft itself, which is unnecessary and uses too much RAM.
What could be causing this variable to be set? (Windows 8.1 64-bit, Java 7)
You probably have a Razer device. Their god-forsaken software secretly adds _JAVA_OPTIONS, but only when launching games, so you won't even see it from CMD. Ideally uninstall the software, and maybe splash some holy water on your PC. Failing that, you can probably get by with shutting down Synapse and restarting minecraft.exe
Found (eventually) here: http://www.minecraftforum.net/forums/support/unmodified-minecraft-client/2183431-_java_options-picked-up-without-existing#reply