This looks a lot like it may be data sampling. Do you see a yellow shield at the top of the report when the segment is applied? If so, the data is probably sampled. You can click the shield to see the extent of the sampling.
The reason you don't have a problem before applying a segment is that the top-level reports are all pre-calculated. Adding a segment ...
You have probably set "skillatwill.com" within your View settings, as Default page. This gets appended to all pages, that end with / Try to clear this field. Please note, that this will not fix already collected data.
There is really no way for you to track down who owns this service account. The only way you can see it would be to login to the Google account that has access.
The best thing you can do would be to not the service account email address and send an email around the company seeing if anyone knows who owns it.
Optionally you could also remove it and wait ...
The only way that i could think of that you could do this would be to use the Google analytics api. It would allow you to request the data you need for all of the views you have access to.
The google analytics website will only allow you to analyse across a single view you cant create reports across views.