The GPS circuitry is VERY sensitive to noise and must be well shielded. This is the reason we added a shield over the CPU, memory and power supply on the 410c DragonBoard, noise was escaping from the CPU and interfering with the GPS. The SBAS signals are much stronger than the GPS signals, and at a slightly different frequency. If you have a noise source (lets say the display as an example), it could have a spur in the GPS band and hence jamming the GPS, but not affecting the SBAS signals.
Did you follow the layout guidelines for the GPS section of your board? See chapter 6 here: https://developer.qualcomm.com/download/sd410/apq8016e-processor-design-guidelines.pdf The I/Q lines from the WGR to the APQ are particularly sensitive and must be well guarded from electrical noise.
Did you select a high quality crystal for the board? If you used a low quality crystal, or a MEMs oscillator the GPS will not work. See the app note on Crystals here: https://developer.qualcomm.com/download/sd410/gps-quality-192-mhz-2520-package-size-crystal-and-thxtal.zip
As a first start I would suggest you test your software and antenna on the 410c DragonBoard. Instructions for connecting an external antenna to the 410c DragonBoard are here: https://developer.qualcomm.com/download/db410c/adding-ufl-antenna-connectors-and-validating-gps-android-application-note.pdf
Full disclosure: I am an employee of Qualcomm Canada, any opinions I may have expressed in this or any other post may not reflect the opinions of my employer.