Unfortunately, yes. Game Guru has no way of separating out game projects. I've had to copy installs and rename them to have separate projects with different custom scripts. But if you just have newly created scripts for each project then it shouldn't be a problem. It's only a problem if you're modifying default scripts and don't want the same behavior across multiple games.
System Specs: OS - Windows 7 Home Premium 64-bit SP1, CPU - AMD Phenom II X4 945, 3.0Ghz, RAM - 8Gb DDR3, GFX Card - 2048MB NVIDIA GeForce GT 640, FPSC-R Version - Beta 1.0085