Designer can also do the nds2nds certificate stuff as I recall. There is also a TID (3578820) duplicating some older documentation (www.novell.com/.../agy16jv.html that discusses how to do this with ConsoleOne.
Going to the root of the problem plugins in your install of iManager may be broken. This can be fixed by manually removing the plugins that cause problems and reinstalling them. Manually removing can be done with something like the steps in TID# 10096957. It is often easier, especially with huge plugins like IDM's, to just reinstall iManager. Try removing the plugins via iManager first as well and then going through the manual method for anything that might have been left behind.
A last option is to have a version of iManager 2.7 Workstation around. Personally I use this tool exclusively except when testing server-specific issues and would highly recommend it for use whenever possible. The documentation talks about it and the install is simple (extract the archive and run from ./imanager/bin/iManager.(sh|bat) (depending on platform). The download for iManager Workstation is in the exact same place as the server-based versions and the plugins are all exactly the same (the plugin installation is also the same). Using this version of iManager you can do all the same administration of IDM you are used to but without involving the server's iManager version. This will at least let you rule in/out iManager or IDM as the source of the problem.