Sous vide over cooking toughens meat? I'm new to sous vide cooking.  The equipment I'm using is a Ronson slow cooker
connected to Sous Vide Magic PID controller, no bubbler.  No vacuum sealer.

I calibrated the SVM temperature reading to boiling water, and it was very
close (99.9 oC).  I then "auto-tuned" the PID.  The end result is that it
takes a long time to get up to temperature (/slow/ cooker), but holds it
within 0.1 oC once achieved consistently.

For my first experiment I wanted to try Douglas Baldwin's Flat Iron Steak
recipe. (12hr @ 55 oC)

I chose three well marbled blade steaks (cheap cut) with a little bit of bone
in the centre.  Each steak was individually sealed in a zip-lock bag using the
water submerge method Doublas Baldwin recommends.

The first day I cooked them for 10 hours (not 12, it was dinner time, and I was
impatient :( ).  I quickly seared the steak 30 seconds per side in a very hot
pan and rested it for 3 minutes before serving.  It was very tender and had a
beefier flavour than any other steak I can remember.  But there were some
tougher bits around the sinew, but still edible.

I left the other two pieces in the fridge over night and continued cooking one
of them for 10 hours the next day.  To my surprise after 20hr total of cooking
at 55 oC, this piece felt tougher and more rubbery than the first, and the
sinewy bits were distinctly even tougher.  Does anyone have an explanation for
this?

I know thickness in a slab shaped piece of meat is most crucial in determining
cooking time, and each of these steaks was about 15mm thick (so not very
thick), so potentially even 10hr was too long?
Anything you salt will firm up in texture over a period of time. I suspect that since you cooked these with seasonings and then chilled and left them in the fridge before reheating an eating they firmed up a great deal in the fridge. 

If you check out this blind tasting conducted by Dave Arnold at Cooking Issues you'll find some more detailed info about this topic. The gist of it is that for cook-chill-reheat purposes you shouldn't salt the meat before searing. For cook-direct serve meals your just fine doing it that way. 

http://www.cookingissues.com/2011/10/12/to-salt-or-not-to-salt-thats-the-searing-question/