One annoying thing in GNS3 is that sometimes after you configured SSH in your routers it stops working after reload. The problem is the key isn't stored in NVRAM, so after reboot, I have to regenerate them every time.
There is a workaround of this problem - open .net file of the GNS3 project and delete
"cnfg="
lines from the routers configuration. It should solve the problem permanently.
Happy routing :)