Sean,
Your tiles will remain in the same exact location because they are given real world coordinates. I have taken TransDEM routes generated by someone else, chopped parts of that route away and merged in a route that I created. There was little if any noticeable difference between which route ended and which began.
You might also find this information interesting regarding Canadian data. The source of your data may explain the anomalies you are experiencing. This is from the TransDEM user manual on pages 179 - 180:
Canada
The Canadian government provides DEMs and topographic maps in an even more
convenient way than the geo servers mentioned before.
All web links verified at the time of writing (12/2015).
TransDEM directly supports Canadian DEMs of type CDED and topographic maps in a
variety of formats, all available from
http://geogratis.gc.ca/geogratis/search?lang=en.
DEMs and maps from these sources have the same sheet lines, so DEM and map will be congruent.
The largest scale maps are 1:50000. Matching DEMs have a resolution of 0.75 arc secs (about 15 x 23 m at 50°N).
Maps
At the time of writing topographic suitable maps for TransDEM are offered as
● Toporama, downloadable GeoTIFF images for automatic georeferencing.
● Toporama WMS, compatible with TransDEM client.
● CanMatrix: downloadable full map images with legend in GeoTIFF format for
automatic georeferencing.
● CanTopo: downloadable full map images with legend in GeoTIFF or GeoPDF
format for automatic georeferencing.
● CanVec, downloadable multilayer vector data in ESRI shape format.
Raster maps are based on NAD83 datum which is equivalent to WGS84 for TransDEM
purposes.
Toporama
Downloadable Toporama raster maps come in UTM and lat/long projection. For
TransDEM, choose UTM. Format is GeoTIFF and georeferencing in TransDEM will be
automatic. These are margin-less maps but detail is not at maximum for 1:50000 scale.
Toporama WMS
Toporama Web Mapping Service can be accessed with the TransDEM WMS client. The
URL is
http://wms.ess-ws.nrcan.gc.ca/wms/toporama_en
CanMatrix
These are hi-res printable maps with a legend and margins (map collar). There is more
detail than in Toporama. They come in UTM coordinates and GeoTIFF format for
automatic georeferencing but need to be pre-processed due to their size and the margins.
CanTopo
This is a new generation of hi-res printable maps with a legend and margins (map collar).
CanTopo is available in GeoTIFF or GeoPDF format for automatic georeferencing but
needs to be pre-processed due to its size and the margins. GeoPDF comes with a “neat
line” to enclose the map frame.
CanVec
CanVec is multilayer vector data in ESRI shape format. The level of detail is equal to
Toporama. TransDEM can read and use the data but cannot distinguish the layers. The
recommended way is to use one layer at a time.
Note: As with all vector data in TransDEM, a DEM or another map of the area has to be
loaded first.
Documentation for the CanVec layers can be found here:
http://ftp2.cits.rncan.gc.ca/pub/canvec/doc/CanVec_feature_catalogue_en.html
The railway layer is coded *_TR_1020009_*.shp
DEMs
Canadian DEMs of type CDED have their own format, which is of file type .dem, but
different to MicroDEM .dem. TransDEM supports CDED type .dem, but file type needs to
be set either explicitly to CDED or to “all elevation data”.
These DEMs have the same naming scheme as the associated maps.
CDED DEMs are in geographic coordinates. TransDEM automatically converts them to UTM, a procedure similar to handling SRTM DEMs.