Hello Phil,
Currently, Light Coverage Profiler does not give noticeable benefits when profiling a .NET application - it works fine only for native applications. We will try to improve the situation in the future.
When profiling by lines, AQtime instruments every code line by adding special service code that is used to collect profiling information. So, if you have some fast code lines that are executed many times, you will get a noticeable overhead because of AQtime's service code functioning. This is what happens in your case.
At the moment, we can't suggest any solution to improve the profiling speed. Sorry.