Without knowing exactly what you have it is difficult to troubleshoot.  Is the membrane covered with ballast or exposed?  Where is the roof insulation (above or below the slab)?

Are you going to patch? Remove and replace the existing roof?  Put a new roof over the old?

For new construction, my company has had good experience with Hydrotech 6125 and  multi-ply (usually two-ply) Atactic Polypropylene (APP) modified bitumen systems such as the Performance Roof Systems by Derbigum. 

Hydrotech is a hot appled liquid "rubber" that fully adheres to the substrate and is generally covered with insulation and ballast.  APP are heat welded systems installed over mechanically fastened insulation boards.

We do not have a lot of confidence in exposed, cold applied "rubber" coatings. Your roofer may recommend using sheet material over the existing.  Has it been re-roofed before?  if you use a sheet material (or any surface membrane), protected walkways for maintenance shoud be created.  Are you in an area where uplift is a problem?  That could make sheet material a problem.

In any case, you should hire an experienced roofing company for major work (minimum 10 years) who offers good a guarantee and have the manufacture's rep sign off on the roof before installation.

Good luck,

Bruce