Shouldn't matter how they pay. My guess is maybe another store is happening causing the cb_gifts value to be overridden. Do you have any auto actions acting on CBSubs payment triggers? If so try turning on Reload User under Parameters for those auto actions so it has an up to date user object before it stores or use the store directly functionality for field actions (should be on by default).

As for your question regarding CB Auto Actions yes you can use it to update cb_gifts if you wanted to. Is this a subscription plan or a merchandise plan as that'll make a difference in how to set this up.

You can use the below in CB Auto Actions to implement any auto action you like on plan activate and deactivate states in that case.

Plan Active
Global
Triggers: onCPayUserStateChange
User: Automatic
Access: Everybody
Conditions
Condition 1
Field: Custom > Value
Custom Value: [var3]
Operator: Equal To
Value: PLAN_ID_HERE
Condition 2
Field: Custom > Value
Custom Value: [var2]
Operator: Equal To
Value: A

Plan Expired
Global
Triggers: onCPayUserStateChange
User: Automatic
Access: Everybody
Conditions
Condition 1
Field: Custom > Value
Custom Value: [var3]
Operator: Equal To
Value: PLAN_ID_HERE
Condition 2
Field: Custom > Value
Custom Value: [var2]
Operator: Not Equal To
Value: A

Be sure to replace PLAN_ID_HERE with the actual id of your plan as found in CBSubs > Plans. In your case you'd just use the Field action and adjust the fields value however you like.