You did not scan the same file.
The file I scanned was one of the files downloaded by the program itself and placed in the "updates" folder
Filename: 1c3e6764-8c6e-45fc-aeae-c3b01f3cdbf3.exe
SHA256: aea6ceba23621f56bec0c47e0053aa8a976a949294312ddbeaae82558eaa8538
Link to scan: https://www.virustotal.com/en/file/aea6ceba23621f56bec0c47e0053aa8a976a949294312ddbeaae82558eaa8538/analysis/1434548903/
Edit:
Here is a log of the scan that found the file
Malwarebytes Anti-Malware
www.malwarebytes.org
Scan Date: 2015-06-17
Scan Time: 14:00:00
Logfile: test.txt
Administrator: Yes
Version: 2.01.6.1022
Malware Database: v2015.06.17.02
Rootkit Database: v2015.06.15.01
License: Premium
Malware Protection: Enabled
Malicious Website Protection: Enabled
Self-protection: Enabled
OS: Windows 7 Service Pack 1
CPU: x64
File System: NTFS
User: Fluffo
Scan Type: Custom Scan
Result: Completed
Objects Scanned: 844989
Time Elapsed: 1 hr, 42 min, 19 sec
Memory: Enabled
Startup: Enabled
Filesystem: Enabled
Archives: Enabled
Rootkits: Enabled
Heuristics: Enabled
PUP: Enabled
PUM: Enabled
Processes: 0
(No malicious items detected)
Modules: 0
(No malicious items detected)
Registry Keys: 0
(No malicious items detected)
Registry Values: 0
(No malicious items detected)
Registry Data: 0
(No malicious items detected)
Folders: 0
(No malicious items detected)
Files: 1
Trojan.KillFiles, C:\LaunchBox\Updates\1c3e6764-8c6e-45fc-aeae-c3b01f3cdbf3.exe, Quarantined, [f5d187344149b87e7a3182838d75768a],
Physical Sectors: 0
(No malicious items detected)
(end)