I am having a bit of a problem following your description of the problem.  Let's change the amounts just a bit to make things more obvious.  Let's assume a $5,000 payment against a $3,000 outstanding A/R, with the remaining $2,000 to be applied to a future invoice. 

MCZ said:

I enter the check.  I hit apply all or one (depending on the amount of outstanding invoices that equal $2500) and then select for the rest of the money to be used for future invoices.

This is correct. It causes the remaining $2,000 allocation to be assigned to Suspense since there is no way to know at the time what it will be paying.

MCZ said:

In the box, the amount shows as applied.  However, I cannot click the box AT ALL to allow me to apply that $5000 check.  If I create a bill and print a bill and then try to apply it or if I create a bill and apply it right away - neither option allows me to apply the $5000. 

This is the part I am unclear about. When you issue the next invoice for that client, the remaining $2,000 should be automatically applied to that invoice. I.e., taken out of Suspense and allocated to fees vs. expenses as per the invoice that was just approved.

I am particularly unclear which "box" you are referring to, and why you want to apply $5,000 and not the remaining $2,000.

MCZ said:

I'm starting to feel like Sage wants me to have to upgrade to the next timeslip package because this only started happen, like I said, in the last few months.  I have been using timeslips since 2013 and never had this problem before.

Nope, that's not how it works.  Sage does not have the ability to cause a v2016 user to start having trouble after a given amount of time has passed just to cause them to purchase an upgrade.

It sounds like you are hitting apply all and then trying to apply it again. Can you just try going to do your apply without hitting apply all first?