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Does the USB hub work OK on the "charged" batteries if it is the only device connected and powered by the batteries? If so, the problem points to noise introduced on your DC power line. The noise can be introduced by your other devices such as laptop which incorporate switch mode power supplies. One of frequency of the frequencies of your equipment switch rates must be similar to that of your hub. Since the problem goes away after a period, I'd guess that the laptop is the main protagonist since it uses more power. At some arbitrary frequency, the switch modes will effectively use an on-off switching ratio determined by the input voltage and power drain. As the battery voltage droops, the on-off ratio adjusts to provide a constant rate of power to the laptop. This also alters the switching frequency slightly as it does so. (Or at least the complex components generated in the switching process) When the system haseen on for a while, the generated noise spikes on you DC supply do not upset the hubs operation.
The cure can require RF filtering of your DC feeds to the various devices. This includes maybe ferrite inductors placed over the cables (both positive and negative) and by putting capacitors across the + and - lines near each device. There should be two layers of capacitance used. One set that has some thousands of microfarads in value (to smooth out larger bumps in the levels) and some smaller values say 100 picofarads as well. These will smooth out the shorter RF spikes that the bigger value caps cannot.
Another aid in the noise reduction is to run your devices in a "star" feed from the battery. Each device to have its own direct feed to the battery. This should minimise noise gernerated by other devices getting on to the sensitive ones.
HTH
Brian
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