115 Brake MC question

["Dean Mericas" <dmericas@domain.elided>]

I flushed out the fluid in the brakes on my 2000 GTV recently, and it developed an odd symptom that I'm hoping someone can help me diagnose.
 
Prior to flushing, the brakes worked fine.
 
After flushing, when I apply the brakes coming to a stop, the pedal goes down quite some distance (~2/3 of the total travel) and feels a bit soft.  Letting up and reapplying the brakes results in a hard pedal, with what I'd judge to be a normal amount of travel.  The brakes appear to stop the car just fine, but the double pump routine has me worried.  I am fairly confident that there is no air in the system.  I suspect that the brake bleeding process did in one or more seals inside the master cylinder.  I'd like to get a second or third opinion before I replace or rebuild the MC.
 
Thanks,
 
Dean Mericas
Ann Arbor, MI
1974 2000 GTV
1965 TR4

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