Don't go through the painful process of re-installing all kinds of stuff, I'm pretty sure I know exactly what's happening.
Make absolutely sure you're not scanning both the 32-bit and 64-bit versions of Stutter Edit. If you do this, there's some crosstalk between the settings due to the plug-ins having the same CLSID. It's a complicated topic and one that we're looking to have fixed in the forthcoming update. (It's also relatively unique to Stutter Edit due to how it names its .dll files).
Anyhow, try removing the 32-bit scan path to Stutter Edit (if there is one) and then scanning again. The point is to only be scanning the 64-bit version. Afterwards, try configuring as instructed by iZotope's document.
If that doesn't do the trick, you might have to take some more specific steps (be very careful though as it involves the registry). Here's what I recommend:
1) Open the registry editor by going to the Run prompt and typing in: regedit
2) Remove all references of Stutter Edit under HKEY_CURRENT_USER\Software\Cakewalk Music Software\SONAR Producer\Cakewalk VST X64\Inventory and KEY_CURRENT_USER\Software\Cakewalk Music Software\SONAR Producer\Cakewalk VST\Inventory
3) You may have 4 entries under this path. If so remove them all. (Note that you can also just rename them)
4) Afterwards, make a point to exclude the 32-bit version of Stutter Edit from your VST Scan Paths
5) Re-scan your plug-ins
6) Added Stutter Edit as an Audio Effect and then go to the VST Plug-in Properties and Configure it as a Synth
7) You may need to completely close and re-open SONAR for this to take affect (we're looking at having this fixed as well)
8) Try inserting Stutter Edit as a "Soft Synth" to the FX bin of an audio track now
Hopefully at this point the settings should stick. Let us know if you make any progress!
Best regards,