Your VB.NET program is very likely to be running in 32-bit mode and will start the 32-bit version of cmd.exe. The one from c:\windows\syswow64 instead of the one from c:\windows\system32 that you used before. Getting BadImageFormatException starts to become likely.
Project + Properties, Compile tab, set the Target CPU to AnyCPU and untick the "Prefer 32-bit" option. On older versions of VS click the Advanced Compile Options button to get to the setting.