In terms of total number of flop movies as lead actor the record goes to Mithun Chakraborty.
Mithun was largely known for small budget movies which often recovered it's money from small centres but the business in Bombay and Delhi Circuit was low. So for the film analysts many of these films were classified as flops and disasters. Adding to the woes he had dozen movies releasing every year which meant he had multiple releases at the same time impacting their own business. So he had dozens and dozens of flop movies in the 90’s and early 2000’s. He must be one of the rare actors to have more than 200 flops as lead actor.
In terms of percentage of flops i think the record will go to Raj Babbar who has worked in around 225 movies but may not have given more than 25–30 succesful films with a staggering 90 percent failure rate. Naseeruddin Shah also has similar proportion of flops but he was an art film actor and his films were not made with commercial purpose. Dharmendra has also given around 180 flops and Jeetendera around 130.