I noticed while getting all my Reputations to level 6 that despite doing one half at the same time and then i start doing the other half of the Reps at the same time once i got the first ones to level 5, they all should have the same amount of Reputation points as each other, but they don't because i'm not always getting Rep points and rewards that come with the daily and hourly when i collect them after they're completed.
I finally looked down at the chat box while collecting the daily for all my Reps and yep... there's a bug where it doesn't always give me the rewards and no doubt the Reputation points too when i collect them. Some of them have the same amount of Rep points but the others all have different amounts, it doesn't collect because it thinks i have no space in my inventory when i do, but that's not correct because the reward is Dilithium Ore and Reputation points, that stuff doesn't go into the inventory.
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It's also worth noting that the Rep Points themselves don't ever show in the chat log.
I consistently work on them all at the same time, first i collect then start all the Daily's and then start all the Hourly's which you do three times a day, but most of them have inconsistent Reputation points. Some are behind about 4,000 - 5,000 less Reputation points and it's also a bit inconsistent where it should be from the Hourly's some have 800, some 400, some 200.
I started on 8 of them and only 3 of them have the same amount of Reputation points while the other 5 Reps are inconsistent the game has not given me both a Daily and an Hourly on those.
The other 5 have about the same but didn't give the one on Gamma yesterday that's at 119,400 while the other four are at 119,800. Since i've done all the Reps at the same though they should have the same amount as each other, but it just may not always collect. I might still be getting the Dilith Ore but yesterday i might not have for Gamma, i don't know how often that error comes up cos i've only recently setup the system into the chat box to reduce the amount of tabs i had but it definitely didn't give me one of the Hourly's.
I noticed it may stall for like 10 - 20 seconds when you start the Daily's or Hourly's too so perhaps that is what's causing it not to collect, don't know though but it's definitely not.
On top of that, ever since the devs did the anti-rubberbanding measures the minigames like Reputation are often sluggish and even get stuck until you change maps or log in the next time. I am almost always seeing one or more of the reputation runs hanging at "20hrs" and while they usually start after a map change sometimes they don't and start up the next day which loses a day's 'work' on the effected rep time-wise since the cooldown starts then instead of the day it was supposed to start.
In the long run it taking an extra day or so is all a drop in the bucket.
You're confusing Reputation Points with Reputation Marks.
Marks are used in the projects to increase the Points. As your Points increase, you unlock the Tiers in each reputation at 5000 (Tier 1), 15000 (Tier 2), 32500 (Tier 3), 60000 (Tier 4), 100000 (Tier 5) and finally 250000 (Tier6).
The reputation projects award 2500 points for the daily and 200 for the hourly.
If you've previously reached Tier 5 on a character, all other characters get that reputation 'sponsored' which doubles the amount of points received - 5000 for the daily and 400 for the hourly.
Unless you really want the stuff from the reward boxes or the dilithium, I'd suggest ignoring the daily projects as they have high resource requirements for little progress in the reputation. The Daily project uses 30 marks and rewards 2500 points yet the hourly project uses 15 marks and rewards only 200 points, assuming the Reputation is unsponsored. This is 50% of the resources used for the Daily with only 8% of the rewards.
Try this.
Type /lootcancel or /loot_cancel in the chat box and press Enter. It sometimes happens that item rewards get stuck in a temporary queue, and this should clear that queue.
Also, as far as I remember, you can only collect 3 hourly projects per day.