Hi!
I have a ClickOnce application (app1) that calls dlls from another Solution (app2). I recently updated this application at one customer and a strange thing occured.
He got the new version (publish version was correct in control panel/add remove programs) of app1 and the application version was correct as manually inspected in the application. But the dlls called from the referenced solution (app2) was still the old ones.
We deleted all files in C:\Documents and Settings\username\Local Settings\Apps\2.0 and installed again. This time there was no problem, the correct dlls were called.
One thing to mention is that the version numbers are completely different in the new version since we changed this while upgrading from VS 2005 to VS2008. Old / new published version: 1.0.0.6 / 1.9.1.6.