I'm not an expert so I hope someone will come along and agree with or correct this statement.
SCRA doesn't eliminate the late fee for covered borrowers, but requires that the rate be lowered to 6%. If you use a 6% rate and still charge a late fee, this has the effect under SCRA of you charging more than 6%. So during the period of active duty, you can't charge both 6% and the late fee.
Since the three late charges on the account were before the period of active duty, I think it is OK for them to remain on the account.
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And where is Superman when I need him?