Ok, so there are really only 2 possible scenarios then.
1.) What you see is all thats being returned from the engines and the rank tracker is reporting everything it sees.
2.) Everything is being returned from the engines each time and the rank tracker isn't displaying all the data.
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In scenario 1, which is the most likely, your seeing what is returned. Meaning a proxy went bad and a term got skipped, or it got blocked and thats all the results it could get before it got blocked etc.. This is most likley the case, so you could try a sample run with a 65 delay and 1 connection and no proxies. Does this work on all terms? You could try different proxies, lower connections etc...
This is most likely the case.
In scenario 2 the engines could be returning different pages. Meaning the plugin uses markers in the code to extract data. If google decided, for example, to return all sorts of different page layouts, then sometimes scrapebox would not be able to extract all of the data or any of the data depending on the format. Engines do run tests with new formats in small groups of locals etc.. so this is possible, especially if you happen to be getting a test group for some of your proxy ips but not others. It would explain the randomness.
While this can happen, based on experience, there is about a 2% chance this is the issue and a 98% chance its somehow related to scenario 1 where Ips are being blocked/banned/going bad and not retriving all the data and the term is getting skipped part way thru or completely.
So trying different proxies, trying with a delay an no proxies, trying with proxies and a delay so its not to fast, trying with lower connections etc... would all be the things to test.