After some more researching I've found a similar problem reported on MyEclipse forum which led me to think that the problem could not be STS but Eclipse itself. With that in mind I finally googled to Anil Samuel blog who faced the same issue.
The workaround is simple, just open .project file on your WTP web project and remove the following XML blocks:
That will fix the issue between STS and SVN.
Well, do you think it should be reported as a bug?