I have discovered the location of the host keys which are causing some SSH problems for those who have 2.0 jailbroken. However, I can't test my findings, so the instructions will be a bit rough and I cannot guarantee anything.

*This is for WinSCP users only. I can modify this guide for those with CuteFTP Pro, but that will have to come later.

1. Create a System Restore point. Open up the Start Menu and navigate to All Programs > Accessories > System Tools > System Restore. We'll be tweaking the Registry, so it's best to be safe.

2. Click Start, then Run and enter "regedit", without the quotes. 

3. Navigate to
Code:
 HKEY_CURRENT_USER->Software->Martin Prikryl->WinSCP 2->SshHostKeys.
There should be a list of keys. 

Here's where things get sketchy. 

4. Once again, we will take a precaution. Select all of the Keys, and then go to File > Export and export the keys to a safe place, just in case.

5. Delete all the Keys.