It started having problems when a GUI was added to make it easier to use. The GUI needs to use the API from outside the bot thread, which posses problems because a thread safe API that works out of process with the client is pretty complex. It's also why the bot doesn't handle changing characters and reloading settings correctly either. The information needed for that stuff, is not valid at certain points in time, so you have to cache the info until it's available again. When it is available, the bot might already be doing things using the old settings. It's a bit of a mess to work around, so that's why it's not fixed yet; it requires changing how some of the GUI stuff works.
When it comes to the Gem Leveler, as long as you don't change your gems around (restart the bot if you do), all you have to do is uncheck all gems and the plugin, then recheck the ones you want and it should start working again. That is the best work around for now, as while a better Gem Leveler is certainly desired, there's a lot of other things that are being worked on instead that would be much better to have working (next beta includes some of them if you check revision guide).
The Item Filter editor is the other thing that is in need of some reworking. We haven't forgotten about them or are just ignoring those issues, but priority wise, trying to address the bigger issues that affect the bot in much more significant ways takes precedence. That, and the fact PoE is rolling out patches as frequntly as they do forces us to spend more time in maintenance and compatibility areas rather than just being able to improve existing features.