The CompuTrainer, by nature, will transition from grade to grade very smoothly even when changing from a negative grade to a positive grade.  The 3D software on he other hand had another need -- making the grade changes look good on the race screen.  To accomplish this, the 3D software will interpolate (to estimate values of (a function) between two known values) between the known grade sections to make the roadway "look good."  Below is an example of a 1-mile course changing from a 1% grade to a 2% grade in the two formats:

CRS format:
Distance  Grade
0.0         1.0
1.0         2.0

3DC format:
Distance  Grade
0.0         1.0
0.1         1.1
0.2         1.2
0.3         1.3
0.4         1.4
0.5         1.5
0.6         1.6
0.7         1.7
0.8         1.8
0.9         1.9
1.0         2.0

So it is clear from these examples how the 3D software attempts to smoothly transition between these two grades.

Elevations in 3D
When building seemingly symmetrical courses you may find the beginning and ending elevations do not agree.  For example, say you add a 1/2 mile section of course at 2% grade beginning at 0 feet elevation and then add another 1/2 mile section at -2% grade; you'd expect these two sections to cancel each other out and end at zero elevation again.  Right?  In fact what you'll find is the ending elevation being much higher than the starting elevation.  This is due to the interpolation required to go from a positive grade to a negative grade.  In order to do this the elevation will rise slightly before beginning to descend.  The illustration below demonstrates this:

If you want to elevation to come out close to the same point as the beginning, you would want to add short course sections (transitions) between grade changes.  By doing so you allow the beginning and ending grade of a particular section to be the same grade (no interpolation) and the grade will be consistent throughout this section as well.  The illustration below demonstrates this:

Granted, courses like this don't look as good in the 3D software (real roadways are rarely so unchanging), but if there is some need for steady grades, this is the way to do it.

Other 3D Course Differences
With the introduction of DeLorme Topo Course Creator, courses are now more complex than ever.  Some of these courses will have thousands of legs, or sections as well as having turns and turnarounds you could not build within the 3D software.  Along with these courses come some odd graphics, because the 3D software was not designed to loop back on itself or cross over itself.  There is very little that can be done to make these look better.  We build courses on the fly in order to allow the unlimited course selections so favored with RacerMate products, so if two sections of roadway share the same spot in memory, they will both appear.  Great lengths were taken within the course building interface of the 3D software to eliminate these graphic oddities, but the ability to add so many courses outweighed the concern for minor graphic oddities.