Unfortunately, this has been an issue for a long time and Microsoft hasn't addressed it yet. The problems are twofold:
1) The logo you upload is digitally "mangled" by Microsoft. Not only does it get resized with the quality lowered, but even transparency is removed. I never understood why they felt the need do that, especially with files that are small. I get it if someone tried to upload a 4MB logo but if the user knows how to optimize an image properly, a 36KB file should not be touched by Microsoft.
2) You only get one logo that is used in two places, the Bookings page itself and the automatically generated emails. So if you design a logo that looks good on the web, it may look terrible in the confirmation emails, or vice versa.
So while we love Bookings and its functionality, the programmers have made it unnecessarily difficult to maintain your organization's branding.