There are a few reasons to that:
1. Madhva himself found a deity of Krishna in Udupi, that became the center of attraction for the whole town. "poornavatar" for him meant that he has all the qualities of Narayana.
2. Sri sampradaya started with alvars, some of whom, such as Kulashekharalvar, were worshiping Vishnu and Krishna on the equal basis and did not distingush philosophically who is first.
3. Krishna worship is accepted to be earlier then Vishnu worship, such as in Krishna-Vasudeva traditions.
4. Krishna is a preference of worship for many Vishnu bhaktas, because of personal preference.
Taking four of the above onboard it will explain to you the reasons.
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