The same methods that have already been suggested.
1. Delete innerspace directory
2. Re-install innerspace
3. Re-install latest isxeq2
4. Download the latest version of interface and script dirs from SVN.
Downloading from the craft thread is redundant, as updating from the SVN has all the latest files.
There are still some existing bugs with craft, however issues like you are describing have been fixed for some time. Using the above method will remove any mis-configured settings and give you a clean slate. In most cases, this fixes strange behavior that isn't being observed by more than one user.
Regarding the experimental directory:
A separate tree for these files would have been my proffered method, however I don't have access to create tree's so adding the dir was my best sollution. I also could have just kept versioning over the existing tree, but that would require everyone understanding to extract from update 42 vs current to get the stable release, and I had very low confidence in that going well with a user base new to SVN.
For now, if you want to test the code I'm currently testing and experimenting with, feel free to copy things from the experimental dir to your live directories. Just understand its just what it says it is, and not fully tested. The current versions I'm testing with has functionality to allow eq2harvest and eq2bot to run at the same time, pausing harvest when agro is detected and allowing eq2bot to resolve the aggro issue (kill mobs). Again, barely tested and may not work for you, so be ready to revert to the stable release.