I think I ran into this same problem.
M4 Pineapple, installed the latest update to tcpdump onto the /usb thumbdrive.
Captures are sent to the /usb/... directory...so far so good.
However, when I click on the History tab, and then hover over the download link, it says:
javascript:javascript:location.href='/usb/infusions/includes/dumps/dump_1397667605.pcap'
When I click on this, I'm shown a white page with an 'X' in it.
That's a bummer.
Looking in data.php, it seems that the problem is that $rel_dir is "/usb/infusions/". The path is therefore set to be the above link.
If we change that /usb to /components, then everything just seems to work well and I can download the reports like before.
In /usb/infusions/tcpdump/includes/data.php, I added a couple lines above the line that generates the download link:
$trans = array("/usb" => "/components");
$newrel_dir = strtr($rel_dir,$trans);
echo "<a href=\"javascript:javascript:location.href='".$newrel_dir.............(include the rest of the line).
That's got it working for me.