As some of my last missions with photogrammetry software (even some done with the same pictures that I had previously uploaded and went fine) were failing, I have compared the EXIF GPS data that DJI is writing in the pictures.
Two pictures taken in the same place, both 50m AGL (over terrain)
1st picture - Firmware beta FW_V01.04.0005
---- GPS ----
GPS Version ID : 3.2.0.0
GPS Latitude Ref : North
GPS Latitude : 39 deg 37' 44.82"
GPS Longitude Ref : West
GPS Longitude : 0 deg 16' 27.05"
GPS Altitude Ref : Above Sea Level
GPS Altitude : 50 m

2nd picture - Firmware public FW_V01.05.0030
---- GPS ----
GPS Version ID : 3.2.0.0
GPS Latitude Ref : North
GPS Latitude : 39 deg 37' 39.45"
GPS Longitude Ref : West
GPS Longitude : 0 deg 16' 23.03"
GPS Altitude Ref : Below Sea Level
GPS Altitude : 57.169 m

Moreover, the NEW FIRMWARE EXIF adds the following data:
---- XMP-rdf ----
About : DJI Meta Data
---- XMP-xmp ----
Modify Date : 2014:10:13
Create Date : 2014:10:13
---- XMP-tiff ----
Make : DJI
Camera Model Name : FC300X
---- XMP-dc ----
Format : image/jpg
---- XMP-drone-dji ----
Absolute Altitude : -57.17
Relative Altitude : +49.90
Gimbal Roll Degree : +0.00
Gimbal Yaw Degree : -76.70
Gimbal Pitch Degree : -89.00
Flight Roll Degree : +10.20
Flight Yaw Degree : -78.50
Flight Pitch Degree : +3.50
---- XMP-crs ----
Version : 7.0
Has Settings : False
Has Crop : False
Already Applied : False

The location where images were taken is about 4m ASL (Above sea level) so the Absolute Altitude can never be negative (below sea level) in this place.
And if in the new EXIF the GPS Altitude : 57.169 m must be  the same as Absolute Altitude : -57.17there  must be a SIGN ERROR

These are my findings

I have same problems, all heights are negative because they are stored as "below sea level"

Inside the XMP, there are two parameter. One is AbsoluteAltitutude and the other one is RelativeAltitude. The AbsoluteAltitude is the above sea level altitude, which is also the GPS Altitude in the Exif ( FW_V01.05.0030). The RelativeAltitude is the above ground level altitude, which once was the GPS Altitude in the Exif (FW_V01.04.0005) , but now not there any more. You could keep using the RelativeAltitude as before.

I am having the same issue using Photoscan.  All of a sudden my renders are showing as either above or below the actual height. Screen Grab from 4DMapper

cheryl Posted at 2016-1-19 14:44
Inside the XMP, there are two parameter. One is AbsoluteAltitutude and the other one is RelativeAlt ...

Hi Cheryl
As you say,
Inside the XMP, (...) The AbsoluteAltitude Absolute Altitude : -57.17 is the above sea level altitude, which is also the GPS Altitude in the Exif GPS Altitude : 57.169 m ( FW_V01.05.0030)

As you can see, the height is the same but the SIGN is different. Plus sign is ABOVE sea level and Minus sign is BELOW sea level
I have been chatting with support for some time but they don't seem to understand the error

Today I've taken some new pictures and the GPS height bug has been fixed.

---- GPS ----
GPS Version ID                  : 3.2.0.0
GPS Latitude Ref                : North
GPS Latitude                    : 39 deg 37' 44.64"
GPS Longitude Ref               : West
GPS Longitude                   : 0 deg 16' 30.82"
GPS Altitude Ref                : Above Sea Level
GPS Altitude                    : 59.517 m
---- IFD1 ----
Compression                     : JPEG (old-style)
X Resolution                    : 72
Y Resolution                    : 72
Resolution Unit                 : inches
Thumbnail Offset                : 41984
Thumbnail Length                : 8473
---- XMP-rdf ----
About                           : DJI Meta Data
---- XMP-xmp ----
Modify Date                     : 2014:10:13
Create Date                     : 2014:10:13
---- XMP-tiff ----
Make                            : DJI
Camera Model Name               : FC300X
---- XMP-dc ----
Format                          : image/jpg
---- XMP-drone-dji ----
Absolute Altitude               : +59.52
Relative Altitude               : +104.90
Gimbal Roll Degree              : +0.00
Gimbal Yaw Degree               : +174.30
Gimbal Pitch Degree             : -90.00
Flight Roll Degree              : +7.10
Flight Yaw Degree               : +167.50
Flight Pitch Degree             : -15.30

Pretty sure there was a firmware update that started storing GPS altitude whereas previous only stored baro (relative to take off point) so significant variability in this value can be expected.