Question on Auto-clearing

I have a couple of questions related to Credits which I am encountering in our system :

Whenever credits are transferred from another CA (doc type XF), these are partially cleared up in auto clearing:

In the example below you will observe that the transferred credit has cleared only part of the invoice. Highlighted entries shows the partial clearing.

I observe similar behavior with Security deposit refunds

The clearing variant 001 set in open item management is as under:

Appreciate any advise in analyzing & resolving  this issue.

PS: Amlan / Will : Apologies for incorrect  details of this issue in my earlier thread. Part of the credits seem to be cleared.