if a reinstall of the software fixed the issue it most likely is just the buggy razer synapse program.
realize there is synapse 2.0 and then there are the drivers for the devices themselves. you do not need synapse 2.0 to configure the mouse.
http://www.razersupport.com/index.php?_m=downloads&_a=view&parentcategoryid=214&pcid=213&nav=0,76,229,213
above is the link for just the mouse drivers and not the whole synapse 2.0 program i believe. i have a razer deathadder and am currently testing out the nostromo gamepad and only downloaded the nostromo drivers not the deathadder or synapse 2.0 software. perhaps this may fix your issue.
you also have the option of running without drivers. the keypad on the side of the naga hex is mapped bydefault to numpad 1-6 or number row 1-6 depending on the switch toggle placed on the bottom of the mouse. you can map these keys to skills in game instead of mapping the mouse to the keys defaulted in game. honestly it doesnt matter which but cross-game the prior (mapping skills to the razer buttons in game) is far easier since you do not need multiple mouse profiles. i currently use my razer deathadder without the software and it works great. in fact i have to say it works better than with the software.
one of the few benefits of software is macros and recording them is less than ideal (for my nostromo drivers at least). another is keymapping to non-default keys or functions.
just some ideas...