Brown seeds will give you a brownish gel, I prefer the golden ones only because the gel looks better. The brown seeds work just fine.
It sounds like you probably did cook it for too long the first time.
Depending on how high the temp is, it may not foam up while cooking and yes, constant stirring is fine, but may have hampered the foam.
The second time you use the same seeds, the gel is always thinner.
Yes, you will end up with less gel than the amount of water you started off with...some of it will evaporate as it boils.
Don't give up!