I have sometimes experienced the effect of decreased intrinsic motivation from setting an explicit goal, especially when using extrinsic motivation from Beeminder. However, I found that this effect wasn't inherent, and I could usually mitigate it by reminding myself why I wanted to do the action in the first place before sitting down to do it. The internal dialogue usually goes like this:

• Grrr, it's late, but Beeminder wants me to write a post on Facebook... Maybe I should write one sentence to get the checkmark, and then go to sleep.
• Wait a second, why did my past self want me to do this? Oh right, to improve my writing skills and share my thoughts with my friends. Ok, I feel like doing this now.

I have experienced this motivation problem much more with output-based goals (like "write a Facebook post") than with input-based goals (like "read book X for 30 minutes").