Have you thoroughly cleaned your surface? I am not sure what material you are plating onto, but are you using the right types of material? Some cleaning solutions preferentially expose certain edges which may or may not be good for the electroplating.
I clean using a 4 step process. I use alkaline solution then deionized water followed by ethanol and then deionized water again. I am plating on to FTO glass slides.
have you thought about using a piranha solution? I found that this would make clean surfaces, I have never used FTO before, are you doing it in a laminar flow hood? or just open in the lab? The pinholes can be caused by stuff on the glass or impurities in the glass causing poor electroplating.
After 2nd wash with deionized water, immersed that FTO glass plate fully in propan-2-ol and boil it. When it boil bring out the glass while it hot. Since it is hot, all remaining propan-2-ol is evaporating and you will get nice clean glass surface. I'm using that method to clean glass when I prepare electrodes for solar cells.
If you are using the TEC glass from pilkington (as many do) I can tell you that the FTO has a high roughness (about double the one of sputtered ZnO). This causes pinholes also when I evaporate CdS onto it. The problem is less with other TCO s.