samples outside bounding box and different geographic dimensions

[tariro.nd...@gmail.com]

1. I defined my study area using ArcTool box extraction by mask feature and used this to clip all my environmenta variables to the study area. However when i run Maxent it tell me samplex, y,...n are outside the bounding box and its a significant number of samples. In actual fact the samples lie well within the study area.

2. An error also pops up with some environmental variable screaming they have different geographic dimensions.  How do I go round this? Any help. Thank you in advance