I could minimize my project to reproduce the problem up to a single llb-file. The problem occured now when having this llb and my teststep-vi in the same directory and running the sequence with labview-runtime-adapter.
I got the solution with the help from @Ballington who checked the llb and found the problem:
"After looking at the LLB more closely, I believe I have found the problem. The LLB contains a VI called clear errors, which looks like is it a direct copy of the clear errors VI in vi.lib.
Deleting this VI from the LLB or force compiling it (ctrl + shift + run button) fixed the issue.
This behavior is occurring because the clear errors VI is a dependency of the simple error handler. If the VI you call in your sequence and the LLB are in the same directory, LabVIEW looks to the LLB to load the clear errors instead of the expected location within vi.lib.
This version of clear errors is not compiled in LabVIEW 2011, so the LabVIEW runtime engine is unable to load the VI, and returns the "VI not executable" error.
With the development system adapter, LabVIEW automatically recompiles the VI, which is why you don't see the behavior in that case.
I would recommend deleting this additional copy rather than force compiling, since it is not good practice to maintain copies of vi.lib VIs."
