There really is no "proficient with a weapon of ## size" in the rules (3.5)
From Rules Compendium pg 151:
Inappropriately Sized Weapons
A creature can’t make optimal use of a weapon that isn’t properly sized. A cumulative –2 penalty applies on attack rolls for each size category of difference between the size of a weapon’s intended wielder and the size of its actual wielder. The measure of how much effort it takes to use a weapon is altered by one step for each size category of difference between the size of a weapon’s intended wielder and the size of its actual wielder. If a weapon’s designation is changed to something other than light, one-handed, or two-handed by this alteration, the actual wielder can’t wield the weapon.
A wielder gains no reach from a reach weapon that is too small. No additional reach is granted by a reach weapon that is too big.
Someone who is proficient in short sword can use a short sword be it small, medium, or large and limited by the changes mentioned above.
So for your example.
Halfling (small) rogue can use a medium sized short sword. However it suffers a -2 to hit and the weapon is considered a one-handed melee weapon.
That last bit is also important as this changes things like: effectiveness of Power Attack, off-hand/two weapon fighting.
