Yes, this is to be expected. Intonation needs to be adjusted for a particular type of string set. Changing strings will change the intonation. Its to do with string flexibility. The more flexible a string is, the less saddle compensation it needs. The less flexible a string is, the more saddle compensation it needs. The Living Water strings are obviously more flexible than the Aquila's.
If you want great intonation you need to stick with a brand of strings. Do you like the Living Waters or are you going to change them again?
Flat intonation is slightly better than sharp intonation. Its slightly less obvious and you can bend the pitch of some strings up a little.
The cure is to move the string contact points on the saddle forwards towards the frets but if you refit the Aquila's then the intonation will be sharp. Another saddle may be in order.
Anthony