It's been such a long time that I don't really remember. I think it was an issue with trailing or leading zeroes in the gerbers. I could be mistaken. It's absolutely ridicilous, though. Gerbers, for all their flaws, are the standard and are pretty much the same from any major PCD CAD software. They should have a dedicated webpage on their site which provides you the Gerber specs and the design rules they require. For instance, if they cannot handle traces smaller than 8 mil they should say so on that page.
No PCB fab in Pakistan posts their requirements as far as I know which I just take as an indication that they don't really care for the business.
The PCBs from Smart PCB were okay, while they weren't any issues with them the ones that I have ordered from China (Gold Phoenix) were very good. The ones from USA were amazing (http://www.4pcb.com/). The USA fab as an automated tool on their website where if you upload your gerbers it tells if you have are violating any of their DRC - and to top it off, they give you $100 off if you use that tool! (at least that was the case when I used it)