I have a similar problem with by 220... sometimes it just refuses to start..sometimes it just goes of while riding.. and whatever i do it just doesn't start...then after a while it works smoothly as if nothing ever happened... took it to the service center they changed a few things they are not really sure with the problem is with...
I've been out of town for a while i just ride the bike when I'm back.. so my dad's been riding/fixing it.. and he is irritated with the issue.. he just doesn't trust the bike anymore... the garage person who he has been going to since years.. is not sure about the FI system so he doesn't want to mess with it..now my dad just uses it has sparingly has he wants it.. if u are are able to find a good mechanic or solution to this startup issue it will be helpful...

My bike is 2007 dec model and just been ridden a tad over 10k kms...
Changed the spark plugs, Electricals..

Will update you if i find a solution . . . .

Have got my bike back yesterday, PBK has replaced the fuel pump,it seems it was short. The battery indicator flashing problem is gone and the bike starts ok now but on the way back home all of a sudden the bike started leaking fuel like someone drilled a hole in the tank. It turned out that they forgot to put a clip on the fuel pipe nr the filter and also from the bolts of the fuel pump. I had to break a wire from a banner on the road and tied up the pipe till i could take it back to PBK. After a little screaming the problem was rectified but took a lot of effort for the mechanic to search for a old clip as the PBK store didnt have it in stock !!! Now after such poor service I feel that buying a Pulsar 220 Fi was really a big mistake !! If the service and availability for spares for their own bikes is so poor by Bajaj if wonder wat those Ninja guys must be going through. . . .

A friend of mine had a similar issue with his bike, the problem was traced out to the Roll over sensor. Try getting it checked.

@ sonu : glad to know ur bike is back and fine. I initially suspected the alternator that charges the battery.

Initially i had the same doubt, but never thought in my dreams that the problem would be traced to the fuel pump. . . Anyways All Is Well now(I still have my fingers crossed)