I've never seen this behaviour before, but here are a few things I'd suggest to help to isolate the cause...
1) Try debugging the same project using version SharpDevelop 4.4 and/or 5.2 beta - do they behave the same? Does repairing or uninstalling/reinstalling SharpDevelop 5.1 from the Uninstall a Program window make any difference (if you've created any file or project templates then back them up first)?
2) Is the problem specific to this project? Try downloading and debugging some other projects from github or sourceforge or wherever, preferably of the same project type as yours (Windows Forms, WPF, ASP.net, console application etc).
3) If it's only your project which is affected by this problem, is your project under source control? If so you could try debugging earlier versions of it to help identify the change which introduced the problem. Or if you're able to publish it to a public repository somewhere then I could see if I get the same behaviour on my machine.
4) If all else fails, you could download the SharpDevelop source code, do a debug build of it (you can build SharpDevelop using SharpDevelop), and then use your debug version of SharpDevelop to debug your project. When you run a debug build, it opens a console window in addition to the main UI, which emits lots of logging information. I'm not sure I'd be able to spot an answer in that information, but someone might be able to.
Hope this helps.
Simon