Your problem of different results is most likely due to different font sizes or other settings in the picture and main file. This is especially true if you are using em or ex as placing units. I can't tell more about it without knowing your code.
However, you can avoid this by ensuring identical settings in both files. Should this not be possible you can still compile the external picture to a PDF an include it using \includegraphics. There is a small size overhead coming with it, but it should not be an issue. It has actually a nice speed benefit with larger TikZ pictures.
For external TikZ pictures I recommend the following procedure:
Use the standalone class for the TikZ picture file and then use the standalone package in the main file. This way you can use \input to read the external file while its preamble is ignored or even copied to the main preamble automatically. When the external picture is compiled by its own standalone makes sure it is placed on a tight page using the preview package. The resulting PDF pictures are very suitable to be included into the main document.
I'm currently working on a new version of standalone which gives you an \includestandalone with an option if the .tex or .pdf should be included!
Update Apr 2012:
The v1.0 of the standalone package now provides \includestandalone which works like \includegraphics, but with standalone files (and similar). The package has a mode=<mode> option which controls if the standalone source file is compiled with the main document (mode=tex) or a PDF version is included as image (mode=image). The PDF can also be build if required (mode=build, mode=buildnew or mode=buildmissing).
An important option for this question is obeyclassoptions, which will try to obey all class option used in the standalone file even if this file is compiled as part of the main document and therefore the standalone preamble is ignored. This means if the external files use \documentclass[12pt]{standalone} then a 12pt font size is also used when this file is included (as source code) in the main document.