Well, without seeing your math it's impossible to say for sure what you're doing wrong. Here's the math for me at level 60:
Seal of Righteousness Rank 8 is 67-68 points of damage per proc. At 12 procs per minute, that's 810 points of damage per minute. Add in four judgements in that minute and you're up to 1342 damage, or a bit over 22dps of damage (holy, so it ignores armor). Add in an extra 15% for the talents and you get 1543 damage per minute, which isn't bad.
If you judge Crusader, the damge from SoR goes up to 107-108, and the judgement damage goes up to 173, but you can only judge Righteousness twice per minute, because you need the other two judgements for Crusader. This gets you up to 1636 damage per minute, or 1881 per minute with the Improved SoR and Improved SotC talents. Basically you're getting 31dps of holy damage. (My base character-sheet dps with a two-hand weapon is around 100-110 depending on gear, so this is a significant boost.)
Now, as for Command: With
Malown's Slam (high-end 5-man instance drop, but only a blue and nothing super-special), my weapon damage is 376-461. That's an average of 419 per hit, so 4.8 Seal of Command procs per minute gives you about 2000 points of holy damage per minute. A Seal of Command proc is treated as an extra weapon swing that does holy damage, so it can miss or be parried/dodged, but it can also crit for double damage, so 2000 damage per minute is about what you can expect. So basically, Seal of Command does moderately more damage than the most you can squeeze out of JotC and SoR.
Other advantages:
Mana cost: Doing SoC for a full minute costs you 110 mana, because you can use Rank 1 SoC. (If it gets bugged you might have to spend 190 mana to use Rank 2.) Judging Crusader and using Righteousness costs you 952 mana for one minute of fighting at level 60, and if you judge Righteousness twice per minute as well, you're up to 1635 mana! The highest rank of Holy Light costs 580 mana, so you can see that the SoR method costs you a lot of survivability.
Bursty damage: This doesn't matter in PvE, but in PvP spiky damage that comes in bursts is much better than steady damage, because it catches people offguard and surprises healers. SoC is very streaky, which can be frustrating when you fight for half a minute without a proc, but it's fantastic when you suddenly do 1500 points of damage on a regular swing + SoC crit.
Weapon scaling: When you reach the level cap, the only way to continue improving your character is through upgrading your gear. When you've spent six months at level 60 raiding or PvP'ing and you're carrying around a shiny purple Hammer of Ultimate Pwnage, your SoC will harness all the power of your weapon, while SoR will still be doing the same damage it did when you first hit level 60.
Weapon Procs: Since SoC is treated as an extra weapon swing, it also has a chance to trigger any weapon procs, or proc any enchantments on your weapon (e.g., Fiery, Crusader). I'm currently toting around a
Halberd of Smiting, and I've seen times when Seal of Command procced, and then both the physical swing and the holy swing triggered the weapon proc. That's a rare event to be sure, but basically SoC amounts to an extra five chances per minute to proc your weapon/enchantment.
Basically, the only reasons to use SoR over SoC are:
1) Don't have SoC.
2) Fast weapon.
3) Tanking with Judgement of Fury + SoR, where you'd rather have a higher chance to get a proc so you can be sure of building aggro.
It's kind of unfortunate that it's so cut-and-dry; I really hope the upcoming talent changes add a little more variety.