oh, that sound like it could be a hex or curse. have you checked the integrity of your tower's Wall Of Flames? casting Norton's Malevolent De-Hexer or Affee's Lower Curse Remover should fix it.
have you brought any suspicious artifacts into your tower? the Dark Market is rife with these sorts of things. weird that it only targeted your homunculus though, normally these things spew miasmas or summon lower demons.
once the curse is lifted your homunculus should reform without issue, but he might be a little sticky for a while and his skin will be a little sensitive. supply him with a tub of ashes to use as a dust bath until his skin fully heals.
as for him being angered about the jar, cover the jar with a thick cloth so he calms down.