Not sure what's happening to you, but I never found this boss that hard. You just have to grab the Drug of Thunder (usually when he's facing away from you), then get in one of the bottom corners and blow bubbles while jumping to pop them. When he comes towards you, run underneath him, then back. It takes quite a few hits, but can be done in 1-2 minutes, three tops. No need to let him turn red -- you should pop his bubble first.
This guy has the right idea but his timing could be better, as he's too aggressive a lot of the time and there's no benefit from taking risks. Like most boss fights, the key is to keep the boss's behavior as predictable as possible, and keep your positioning as controlled as possible. When the player in the video tries to pop bubbles in the upper half of the screen, he makes his rate of descent and the boss's attack pattern unpredictable, and risks getting caught by a salvo of hammers in mid-air.
This video is much better, and is pretty much how I fight this boss (I beat Bubble Bobble just a few months back with my wife, but I've been playing it off and on since it came out). Stay low, run behind him whenever possible, and always remember that as long as some of the hammers are still in flight, he won't launch a new attack.