Improving the performance of the Hough transform
Are you using openCV?
Anyway, if you are running an edge-detection, and then the hough transform on the edges, it might help to smooth/blur the edges with some bluring functions. OpenCV got some different ones for that.

In particular a boxFilter with a 2x2 sized kernel, anchor=Point(-1,-1), and normalize=false.
It will hopefully make all the edges "thicker", filling in gaps and inconsitencies in the process.