I read the workaround before in some other posts scattered somewhere. Sorry i didnt found it again so please request for quote.
I post it again cause my opinion is it´s worth sticky, maybe im wrong.

If you want your weapon in an hardpoint of your choice placed, you have to know that the oldest weapon bought is placed on top hardpoint in one section and so on.
Example:
3 Missile Hardpoints at Right Torso
Choosen placement:
LRM 20 topmost
LRM 5 second top
LRM 5 third top
Result:
LRM 5 topmost
LRM 20 second top
LRM 5 third top
Thats because of your LRM 5 is older than your LRM 20.
Workaround:
- Unequip your topmost LRM 5. Your LRM 20 should now be topmost.
- Save (checkout^^) your Mech.
- Sell it or equip it in an other Mech.
- Equip an new LRM 5 and save.
New result:
LRM 20 topmost
LRM 5
LRM 5
I tried this with different Mechs and Weapons but i could be wrong. If anyone can confirm please vote for sticky.
thx