It looks like I fixed the issue that argv0 mentioned, which has been in mIRC for many versions.
I have been unable to reproduce the issue that you have described unfortunately. Was this issue present in mIRC v6.35 as well? Would you be able to find a step by step method of reproducing it? eg. perhaps creating a script that outputs lines (some of which are links) to a @window and then performing certain actions that cause the issue to happen?
