All the following is basically to say, I believe this is indeed a bug with the weapons and not user error in the Viggen.
I have had similar issues
after using ANY A-G weapon properly, after rearming it will not allow me to fire the weapon on the next flight
I put on the safe, I configured the landing, no nav errors, made the references and fixes, no warning lights
Even sometimes turned the nav system and the entire aircraft completely off and back on, inputting references and time so it would still work, it was just like there was no power to the weapon systems, the maverick sight wouldn't illuminate, RB04s and RB15s would range but not come off the rails, bombs refused to drop
The hud symbology and NAV system would work, no warning light on the hud until I was out of parameters.
They simply wouldn't come off in any circumstance except the emergency jettison.
even the fast modes in the ASM's
I also tested purposefully messing up the nav, taking off, landing, then fixing it on the ground, taking off again and the weapons would launch fine the first time, then the bug would occur.
I didn't test A-A weapons
the emergency jettison below the fuel tank release would still work properly though.
Initially all the weapons work perfectly though :) with the Bk90 multiplayer workaround coming it'll be great.