I haven't found that at all. I fly mainly to the EU and have had no problem bringing through empty water bottles.

My last flights were this month and I did Stockholm, Frankfurt and Madrid. Also no problem through LHR. I always fill up in the lounge on my way to the gate. In Germany there was no time for a lounge visit so the gate agent sent me to the washroom to fill up the bottle since they didn't have any water fountains.

No problem in Singapore doing that on a flight to FRA (Nov 2006). In Japan I was able to bring a bottle with water in it through security on my way to Singapore.

I'm thinking the problems you are experiencing are extra levels of security for flights to the US. I know that many airports have an extra level of security for US flights only. Were these all EU to US routes? If so, fly through Canada and save yourself the aggravation.