These results are correct, it's just that the potions are affecting your base skill rather than directly affecting enchantment strength. Enchanting's base skill has a particularly weak* effect on things (and it's non-linear, so only a fraction of that +x% manifests in enchantment strength); it's all about the perks.
The formula is
net magnitude = base magnitude * soul multiplier * skill multiplier *
(1 + Enchanter perk) * (1 + specific perk modifier)
skill multiplier is "approximately"
skill multiplier = 1 + (skill / 100) * (skill / 100 - 0.14) / 3.4
It is the above
skill value that enchantments affect, not the net magnitude. Therefore, your skill multiplier should be
skill multiplier = 1 + 1.25 * (1.25 - 0.14) / 3.4
Plugging that back into the
net magnitude formula we get the following for Resist Fire (
base magnitude = 15%) and Regen Stamina (
base magnitude = 10%)
net magnitude = 15% * 1 * 1.4081 * 2 * 1.25
net magnitude = 10% * 1 * 1.4081 * 2 * 1.25
Like the UESP page said, the
skill multiplier formula was approximate, so I'd say this is close enough. The point is that potions affect your base Enchanting skill, which has a non-linear and weak relationship with enchantment strength. In fact, Enchanting at 100 only grants +25% to enchantment strength over Enchanting at 15 (rather than
100 / 15 = 6.7x), so taking 2 perks and Enchanting 20 is better than no perks and Enchanting 100.
* It actually looks something like this. The above formula doesn't seem to be totally precise, but the gist should be evident:
Notes (as the comments show I should have been clearer here):
+46% = Necromage maximum (5 items of Fortify Alchemy)
+37% = Max with 5 items of Fortify Alchemy (Falmer Helmet + Circlet)
+32% = Max with 4 items of Fortify Alchemy
+25% = Enchanter's Elixir (best non-crafted item)