Looks like nobody's seeing what you're seeing...(?)
GI Javelin (I)
Base damage: 1236 (Level I Javelin weapon damage)
Rank 1 cloak: 1730 (40% more than base weapon damage at level I)
Rank 4 cloak: 2225 (80% more than base weapon damage at level I)
Rank 6 cloak: 2781 (25% more damage than rank 4 damage)
GI Javelin (X)
Base damage: 1546 (25% more damage than weapon at level I)
Rank 1 cloak: 2164 (40% more than base weapon damage at level X)
Rank 4 cloak: 2782 (80% more than base weapon damage at level X)
Rank 6 cloak: 3478 (25% more damage than rank 4 damage)
Seems like it's calculating properly to me...(perhaps reword your findings so we can better understand?)
There is a difference in damage between level I and X, but you won't notice it much except on certain weapons. The Adas, for example, only sees an 83.11 DPS increase (assuming reload cancel, no bonuses in passives, etc) whereas the Raider sees an increase in 245.39 DPS.
Yes, a level X does more damage than a level I weapon, however the results are rather minimal. I'll take a level X claymoar over a level I any day, but a claymoar is a claymoar... the javelin is a javelin, and the harrier is still a crappy weapon. That is all.