Two possibilities come to mind. First, a scaling issue. Second, watching it unrendered.
Can I ask what you mean by a scaling issue, do you mean that the size of my logo is wrong?
Not 'wrong' per se, but not exactly the size you want. Which means you've adjusted the scale of it in Premiere, which could possibly create the jaggy edges you describe.
Can you post a screen-cap of this logo?
What I would do would be to place the CTI over the logo in use, and set the Program Monitor to say 100% (maybe even 200%), and then scroll, as is necessary, so that we can see the logo clearly.
My first guess would be that Jim is correct, and that PrPro is doing a poor job of the Scaling. I am less a fan of PrPro's Scaling algorithms, than I am of Photoshop's. I would always resize any .PSD to what I needed, or as nearly so, as is possible, in Photoshop before Importing and using in PrPro.
Still, it could be something else.
The other's are probably right. One thing you might try to make sure the scaling and positioning is mostly correct is to use Premiere's Photoshop function to create a full screen PSD. File>New>New Photoshop File. This will create a PSd that has the same dimensions as your sequence. Then size the logo the way you want.
Bring it to your timeline and see how it looks. If it's still wonky, take the workspace area bar and render a small portion of your timeline to see if the final output is to your liking. Probably it is.
hope this helps,