So just to clarify a couple things...
1. The "stem" I was referring to is the metal piece that moves up and down to open/close the valve of the tube...it is the piece within the portion of the valve that you are refering to as a stem. I gather we are both using the term correctly but just wanted to clarify to avoid potential for confusion.

2. The longer the section of the valve stem that is unsupported by the rim, the easier it is to bend or break, or even rip the entire valve off the tube. This becomes even more of an issue when using a frame pump to inflate...but I looked up the pump you used and found the Serfas FMP-500 is a floor pump...in this case the recommendation would be to ensure the valve nut is loosened completely and manually manipulate the inner stem to ensure it moves freely and then exercise caution when attaching/removing the pump to avoid damage to the valve.

3. One last thought...the valve only needs to be inserted into the pump head enough so that a seal is made around the valve and the pump head does not blow off the valve while pumping. Jamming the pump head too far on the valve can sometimes cause damage or problems with inflation. If the pump head does not stay put while pumping, enouraging you to press it on the valve further, then I recommend replacing the pump head insert and/or using a length of velcro strap connected to the head wrapped around the tire/wheel to keep the head in position while inflating.

Good luck.

-j