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I have a 2006 Eclipse with about 48,000 miles on it, and ironically, I’ve had to depress the brake pedal further twice in the last month. These are the 1st times this has happened! Unfortunately, it 1st happened right after my 45,000 check-up. Obviously, especially after reading your situation, I will keep a close eye on it. Also, I recently starting hearing a squeak too. I’m not sure if it’s from the brake or the clutch.

There’s air present in a new master cylinder that’s very difficult to get rid of when just doing a regular bleed. When they replaced it, did they bench bleed it?

If not, the way you do it is like this:
clamp it in a vice and attach brake hoses or pipes onto the outlets. You can get some longer metal lines from NAPA with the appropriate connectors on each side and just cut them in half. Then attach and bend them such that they pee back into the master cylinder’s reservoir. NAPA actually sells a master cylinder bleeder kit to do it as well but it has rubber lines. I just like those lines to not flop around to make an unholy mess so use metal lines.
Press the plunger until until you notice that here are no more air bubbles coming out. Install the master cylinder with these brake hoses installed. Once mounted onto the booster, very quickly change the lines out for the real ones, one by one. It will be a bit messy because it will start to leak fluid when you disconnect a line. You may need to top the reservoir off so air doesn’t re-enter the system.

Do you set your handbrake (parking brake) on a regular basis? If you don’t, then try this, pull up and down on the handbrake lever a dozen times or so. Each time you pull up, pull with at least 30 lbs of pull. If you find that the hand brake lever starts to tighten up, that is it doesn’t go up as high toward the end is it did at first, then you have properly adjusted the parking brake. Now see how the main brakes feel.

If that doesn’t work, someone may need to disassemble the rear brakes and check them for proper adjustment and check that the self adjusters are working properly.

I see where Keith is going.
This car has drum brakes?

Some designs of rear discs have to be adjusted as well.

I’m assuming this car has conventional brakes, not the anti-lock version.

I think the master cylinder was bad – common problem for a car of that age – and that was causing the initial symptom. In replacing the MC, either it wasn’t properly bench bled first, or air got into the brake lines and hasn’t yet been properly bled out.

My suggestion: All four wheels need to be rebled. And it has to be properly done, per the manufacturer’s recommended brake bleeding procedure. Find a copy of the car’s shop manual – the one published from Mitsubishi for that make/model/year – and see what it says.

Does the long pedal travel and softness disappear if you pump the brakes?