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Join Date: Jun 2011
Location: Sunnyvale, California
Posts: 1,180
Bikes: Bridgestone RB-1, 600, T700, MB-6 w/ Dirt Drops, MB-Zip, Bianchi Limited, Nashbar Hounder
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I've got threaded and smooth presta stems on various rims. I haven't had any such issues with longevity of the valve base or with pumping, whether it's with portable pump (Zefal HP-X classic frame pump) or floor pump. Both work. I tend to buy whatever tubes I can get on sale, and sometimes, those are smooth stem, 60mm variety with a lot of stem showing for a semi-aero profile rim.
I'm am a bit confused why the tube is not seating correctly. If you don't have a tire, and just have the tube around the rim, will the valve stem/base seat correctly and give you more extension out of the rim? If that's the case, then maybe the tube you have with combination of rim/tire bead makes it unsuitable for your tube. You may want to revert back to some other brand of tire or tube. Or maybe use a rim with wider internal ISO width spec?