When uploading a "Classic" skin with the narrow/Alex type arms (with 3 pixels) everything is peachy keen. However, when you exit the game, upon reopening your "Classic" skin is automatically converted to a wide/Steve type arm, which causes weird graphical errors such as erroneous black or transparent lines. This is really frustrating as the only workaround is to manually re-upload the classic skin every single time you open the game. 

This only affects classic skins. Skins made in the native skin editor carry over the arm size appropriately. 

A recent thread on Reddit that explains the same issue: 

https://www.reddit.com/r/Minecraft/comments/1ger91w/how_come_my_mc_skin_keeps_doing_that/

See screenshots. First screenshot named "NarrowNormal.png" shows what it looks like after uploading a Classic skin and selecting the narrow arms. The second screenshot named "AfterReopen.png" shows what the skin looks like after closing and reopening the game. Notice that the arms are 4 pixels wide, but the 4th row is completely transparent.