Question for you.

You said:

"There are some unexplained variances when reconciling cash Management with general Ledger relevant accounts. "

I know you have posted lots of details. I may have missed something but to me it is not clear which two numbers are not agreeing?

The balance in GL Cash (Bank) account and the ending balance on your bank statement?

If the above is true then I would do the following:
1) Go back to the month when the two were agreeing.
2) From that point onwards find out if there is any journal in GL that has directly touched GL Cash account and is not coming from AP or AR.

When cash account is touched directly by other modules than Cash Management then it becomes a nightmare to do the reconciliation. That is the whole purpose of Cash Clearing account, so that Cash is touched only by Cash Management.

Reconciliation has to be done every period (be it daily or month). One cannot do reconiliation once in a while. Otherwise you have to trace back and see when the problem started.