Did you make your own Localization entry in TranslatedStringKeys and have your skill point to that? You want to be changing where the stuff like "Skill_Flare_Description" and such point to (you can change the Ref versions as well to have the description there, but that doesn't do anything ingame; it looks like the Ref is just meant for the modder's reference).
There are three Localization files that each skill uses (and an extra Ref version for each):
1) Name of the Skill
2) Description of the Skill
3) That extra text at the bottom of the skill saying what the effect actually is
Edit:
Here's the stats for my modified Rain skill, "Healing Rain"
new entry "Heal_Rain_Water"
type "SkillData"
data "SkillType" "Rain"
data "Ability" "Defensive"
data "Element" "Water"
data "ActionPoints" "4"
data "Cooldown" "6"
data "ChargeDuration" "0"
data "Lifetime" "5"
data "SurfaceType" "Water"
data "SurfaceLifetime" "12000"
data "SurfaceStatusChance" "100"
data "SkillProperties" "Consume,100,5,SKILLBOOST_AoE_Healing_Rain;Douse,-1,5,,70"
data "TargetRadius" "15"
data "UseCharacterStats" "No"
data "UseWeaponDamage" "No"
data "AreaRadius" "20"
data "TotalSurfaceCells" "125"
data "SurfaceGrowStep" "5"
data "SurfaceGrowInterval" "150"
data "Icon" "Skill_Water_Rain"
data "DisplayName" "Rain_Water_DisplayName"
data "DisplayNameRef" "Rain"
data "Description" "Rain_Water_Description"
data "DescriptionRef" "Create water surfaces."
data "StatsDescription" "Rain_Water_StatsDescription"
data "StatsDescriptionRef" "Radius: [1]<br>Duration: [2]<br><br>Creates water puddles on terrain, douses fires, and makes characters wet. Water surfaces can be electrified."
data "StatsDescriptionParams" "AreaRadius;Lifetime"
data "FXScale" "100"
data "PrepareAnimationInit" "skill_rain_start"
data "PrepareAnimationLoop" "skill_rain_loop"
data "PrepareEffect" "FX_Skills_Water_Rain_Prepare_A"
data "CastAnimation" "skill_rain_cast"
data "CastTextEvent" "cast"
data "CastEffect" "FX_Skills_Water_Rain_Cast_A"
data "TargetEffect" "FX_GP_Target_Water_A"
data "Magic Cost" "1"
data "RainEffect" "FX_Skills_Water_Rain_A"
data "Atmosphere" "Rain"
data "ConsequencesStartTime" "1000"
data "Skillbook" "SKILLBOOK_Heal_Rain_Water"
new entry "Heal_Rain_Water_3"
type "SkillData"
using "Heal_Rain_Water"
data "Level" "3"
DisplayName, Description, and StatsDescription (not the Ref versions) are the ones that point to the Localization file to use.