It appears that if you are recasting a spell is at a different level then when you originally cast it, it can mess up your resists.
I just redid the spells on my tamer, and ended up with an extra 4 physical resist left over, naked and all the spells removed (either from casting Protection to remove it, with GM resist when the original Protection was cast using only JOAT inscription, or recasting the Reactive Armor/Magic Reflect combo at GM, when the original was cast at 80-something).
So, everyone be careful when messing with the 3 toggle spells.
BTW, the formulas for the spells are as follows:
Reactive Armor: -5 to all elemental resists, +10 Base to physical (+2 per 20 points of inscription* - rounded down always, so total of +20 at GM only)
Magic Reflection: +10 to all elemental resists, -30 Base to Physical (+2 per 20 points of inscription* - rounded down always, so that the penalty is -20 at GM only)
The "Reactive/Reflect Combo": Both spells cast together at same level of inscription.
All Inscription levels: the penalties combined with bonuses end up with a +5 net bonus to all 4 Elemental Resists. The only differences are in the Physical resist column.
0 Inscription (Elf only): -20 Physical Resist
0 Inscription Human, 20 Inscription Elf: -16 Physical
40 Inscription (both races, from here on): -12 Physical
60 Inscription: -8 Physical
80 Inscription: -4 Physical
100 Inscription: Base Physical (penalty & bonus cancel exactly)
Protection: Does the following =
-35 to -30 Resist Spells (-35, +1 per 20 points of Inscription*)
Faster Casting -2 (supposedly, this negative FC can't be raised above 0 for mages by equipment)
Spells can't be interrupted, except by paralysis or having mana drained (as spell - leeching weapons do NOT lower the target's mana, but convert damage HP to the leeched attribute) below ability to cast.
Physical Resist: -15 to -10 (-15 at 0 Inscription*, +1 per 20 points of Inscription)
* Humans treated as if they have 20 inscription for all these spells.
For someone to have a -1 resist bug, it sounds like it was probably involving Protection castings (perhaps involving someone else casting Arch protection)
On the other hand, my bug is probably related to a 5-year old casting of Magic Reflect & Reactive Armor (at 80 skill), that I removed part of last month, and the other half today.