If you are going to direct to merchant, on those searches where you are missing, is there another affiliate showing with that same merchant domain name?
If so, they either have a higher CTR and/or outbidding you and you keep losing what they refer to as the "auction".
If you have your own landing page and domain, then Google may be attempting to abide by your daily budget by spreading your showings over the day so your budget lasts as close to 24 hours as possible.
Turns out, Google often does a rather poor job at predicting how often the real world will search on your terms. Notice the dichotomy between what the "Traffic Estimator" often claims you'll receive in clicks versus what you are actually capable of getting.
For all but the most common keywords, it often necessary to multiply the suggested budget by a factor of 2 or more to ensure your ad will actually show for most searches on your keyword. Unless you're dealing in a highly competitive area where there is enough statistical history to consistently predict the number of searches, I've found you need to exceed any suggested budget to appear with the frequency you'd like.
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