Some time ago I downloaded VirusTotals Windows based tool for uploading samples for scanning (vtuploader).
Out of curiosity I uploaded the the tool back to VirusTotal for scanning and several of VirusTotal's online AV scanners flagged vtuploader as being suspect.
I reached out to the folks at VirusTotal regarding their own tool getting flagged and they responded by saying that it was probably being flagged because it had not been signed.
Only one AV scanner on VirusTotal's site still flags the vtuploader tool today (Baidu).
(I don't know if VirusTotal ended up eventually signing their code or if the AV companies have just now whitelisted the vtuploader tool so it no longer gets flagged.)