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In short, politics.
The Flensburg Government (Doenitz's German government) wanted to surrender to the Western allies (the United States and United Kingdom) rather than the Allies as a whole, primarily because of the Soviet reputation for how they (mis)treated prisoners. To this end, Admiral Friedeburg was sent to Field Marshal Montgomery's headquarters. Montgomery was unwilling to accept such a surrender, but Friedeburg was able to negotiate a partial surrender, of forces in Denmark, the Netherlands, and northwestern Germany, including the U-Boat forces. This had the effect of being a surrender to the Western allies, since they were the ones who controlled or were adjacent to these areas.
Between the May 4 partial surrender and the May 8 total surrender, German refugees and troops frantically tried to reach Western allied lines to surrender; this included several breakout attempts by forces encircled by the Soviets. On May 7, General Eisenhower informed the Flensberg Government that further attempted surrenders by German troops to the Western forces would not be accepted, which lead to the May 8 unconditional surrender of all forces to the Allies as a whole.