When using SSH as the connection for IDEA\'s git integration, IDEA keeps asking to store the host\'s rsa signature in the host key database. Pressing Yes works, but does not
I'm not 100% sure what your problem is related to, but jetbrains has a page in their documentation about setting up ssh keys for git: using-git-integration.html
I'm running idea on a mac and have my ssh keys in the standard unix ~/.ssh and I never get any questions about key stores. On windows you probably should put your ssh keys under C:\Documents and settings\username.ssh
Also have a look at the version control tab in idea for more specific messages when troubleshooting vcs problems.
Have you tried command line ssh to the server, and then accepting the host key? That should store it, as it won't go through some Java/JNI/Windows contortions.