Yep, against a % based brokerage, for some scripts, they will charge you as per quantity. So if the lot size (for small value scripts) is 8,000 or 12,000 or such, the brokerage will be Rs. 1,000+ for a sing lot trade. A lesson learnt, so it is always advisable to check from time to time your ledger and contract note from your brokers, as they can change the terms of brokerage, without you being aware. Caveat emptor, as they say in Latin, let the buyer be aware (always, anywhere, anytime)
Looks like you ve had some bad exp with them.