I'm using the Enhanced Client and what you described is what I was expecting to happen. Here's what actually happened:
1. I had an empty keg and two empty bottles.
2. I made 1 Greater Poison leaving 1 empty bottle and 1 full one.
3. I dropped the full bottle on the keg.
4. The keg filled and I had 1 empty bottle - the one I dropped never came back.
5. I made another Greater Poison, filling the 1 empty bottle.
6. I dropped that on the keg - keg filled, no empty bottles.
7. I got another empty bottle from the chest.
8. I filled that and dropped it on the keg - still no empty bottle.
9. I tried again twice, for a total of 5 bottles before I was convinced that it wasn't working 🙁
10. I came to the forum to ask for help.
Must have been a glitch because I just tried it again today and it worked perfectly.
*5 mins later*
Ack, no it didn't work perfectly! It is happening again!
1. I made Greater Poison, filling an empty bottle.
2. Poured it on the keg - the bottle came back, YAY!
3. Made another Greater Poison - it went straight into the keg, as it is supposed to, YAY!
4. Came here to post my success.
5. Went back and kept making Greater Poison till I ran out of Nightshade, all pouring into the keg as expected.
6. Switched to make a Greater Strength in my empty bottle.
7. Poured it in a new empty keg.
8. Bottle came back, YAY!
9. Made a second Greater Strength, bottle disappeared!
10. Got another bottle, made another Greater Strength, bottle consumed again! BUGGER!
Going to log out and in again and see if the glitch has gone. 🙁
*2 mins later*
Nup, logged out and in again, new bottle, Greater Strength, poured it on the keg, bottle is consumed. ARGH!!