It is likely that one of your controls is using a match rule which changes every session. You'll need to identify that and update it to be more generic. You can usually determine this by simply interrogating the same controls again next to the ones you did previously and comparing the match rules between them.

We are facing the same issue for an windows based application.  When we start the windows adapter to interrogate the objects, fields are identified with green tick mark.  But when we ran the solution or restart the windows adapter under interrogation mode, fields are not idenfied by Pega.  Tried Rematch, Focus and Activate methods but still Pega throws up error stating objects are not identied. 

Best practice when interrogating is to access an application in more than one session using different data each time. This will help you to identify any match rules that may have be context sensitive.

To identify which match rule needs to be modified remember that parents must match before their children can match. Look for the highest control in the hierarchy that does not match. Fix the match rule for that control and then repeat.

One other item that is critical. Match rules must generate a unique match. If you see the warning that your matching is not unique you need to modify the match rules at that point to match only one control. Unless you are using UseKeys=true only one control at a time may match. So if you navigate the application in a different order at runtime than you did at design time, different controls may match.

Hope this helps.