That is because MP can have 9999 as well...  it can't be altered...  only leading 0's would fix that and that would also look a bit crap.  FFX does it this way as well, it right aligns and leaves gaps...  what's good for Square is good for me 

Also felix, there is a pretty easy way to sort that time bar.  The code is at 006DD4EF, depending on what colour it shouldn't be too hard.  You will get a nice blue just by nopping 006DD4F6.  I.e. 
006DD4F6,006DD4F7,006DD4F8 will all read as 90.  That shift can be altered or changed into other code which should give us a degree of leeway.
I can code it to give any colour but it is a bit more work.