platformio-core: Large Teensy 3.1 project builds but does not run

Configuration

MacOS El Capitan PlatformIO, version 2.8.5, installed via homebrew

Description of problem

Building a large (many libraries and code files) Teensy 3.1 project outputs a meaningfully different elf file and hex file as compared to a working one built using Arduino 1.6.7/Teensyduino. The hex file fails to upload via the CLI uploader, but does seem to work in the GUI uploader. Once uploaded the app fails to start, no debug output.

A trivial blink app (using the same platformio.ini file below) works fine on the same system.

Steps to Reproduce

1. Build app via Arduino/Teensyduino. Works.
2. Build app via PlatformIO, generates different elf and bad hex file

If problems with PlatformIO Build System:

Some warnings but no errors in build results below.

The content of platformio.ini:

[env:teensy31]
lib-ignore=extras
platform = teensy
framework = arduino
board = teensy31
build_flags = -DTEENSY31 -UUSB_SERIAL -DTEENSYDUINO=127 -DARDUINO_ARCH_AVR -DUSB_SERIAL_HID -DLAYOUT_US_ENGLISH 
board_f_cpu = 96000000

Source file to reproduce issue: build results: buildresults.txt .elf and .hex files from platformio: firmware.zip Working elf and hex files as built by Arduino working.zip Source files available if you need them, it’s a pretty big project.