I suggest using the MODIS Reprojection Tool (MRT) to properly project your MODIS data. This might solve your alignment issue. Make sure you use the same coordinate system for each file. You can also mosaic tiles and convert HDF to GeoTIFF through its interface. Once you've done that, you can manipulate them further in ArcGIS or ERDAS.
Does the alignment issue exist when you bring the raw HDF files into ArcMap?
MRT can be a bit finicky. You need to have both MRT and Java installed to a folder on your drive without spaces. I suggest reinstalling (or installing) Java and MRT to C:/programs/java and C:/programs/MRT. It can have problems searching for them when they are located in Program Files.
Note that the projection parameters default to the northern hemisphere. If you need another projection, you can reproject in another software package later. There is also an option to batch process your data by creating a parameter file. There are instructions on how to do that in the user manual (page 40). Also, if you add two scenes (or more) from the same day to the input files, it will mosaic them for you.