I only adjust intonation with new strings for that reason. Adjust it with old ones, change your strings and now your intonation is out and you have to do it again. If you change them and it is still flat, you might not have enough bridge for the adjustment. In this case you can, get a "Nashville" style bridge, raise your action, change your string guage or live with it. I have put Guitar Fetish bridges on alot of my Epiphone guitars.
Hopefully the new strings fix it though but if not their bridges are only like $12 and they have the large bushing ones to fit Asain made guitars like Epiphones.http://www.guitarfetish.com/Large-Bushing-Tuneomatic-Style-Chrome-Bridge_p_444.html
PS Not pushing the thing at you, just providing answers to anticipated questions. Also if you did do it realize that it is not necessary to replace the ridged part that fits down inside ther guitar (Top right in pic). The threaded posts fit right into the existing ones in the guitar and the bridge drops right on. It is a simple job.