This bug relates to
#1580 which as been marked as resolved.
I can confirm this issue happens on the latest version 2.5.1.
If I do a "Add Files..." from the root of the Repository, ignored files are correctly unchecked. But, if I do a "Add Files..." from a sub-folder of the repository, then ignored files are checked as well, which should not be the case.
I've attached a screenshot that demonstrates the problem.
I'm testing Hg and Git as a possible substitutes of SVN, and this only happens with TortoiseHg. All other Tortoise* do not automatically check ignored files.