I have a TeamRaiser set up, and the registrations are synching correctly, but the donations are synching with a different appeal, fund, and/or campaign than we've defined in our donation form.
When a donation is made through TeamRaiser (whether through a participant, to the event, or a team) it will always use the cross reference defined for that TeamRaiser when possible. TeamRaiser cross references take precedence over donation form and donation campaign cross references. It is possible to setup a separate fund for registrations and donations within a TeamRaiser. When editing the cross reference, you will see sections for "The Raiser's Edge Fund (TeamRaiser Upsell)", "The Raiser's Edge Fund (TeamRaiser Registration)", and " The Raiser's Edge Fund (TeamRaiser Gift)" which you can use for differentiating different types of TeamRaiser transactions.