When creating Custom Quarters you enter the start and end date (e.g. Q1 = 2/1 - 4/30). However, the system uses the beginning of each date as in 12:00am or 00:00:00 to run it's calculations (e.g. 2/1 00:00:00 - 4/30 00:00:00). So you will lose any activities that exist between 4/30 00:00:01 - 4/30 23:59:59). They will not count into the next Custom Quarter either as it would not start until 5/1 00:00:00.
This can be worked around (but not resolved) by moving the Custom Quarter end for Q1 out by 1 (e.g. 2/1 00:00:00 - 5/1 00:00:00). Q2 start and end would then be 5/1 00:00:00 - 8/1 00:00:00 HOWEVER this creates an overlap
1) any task/project/hours/etc that occur on 5/1/2017 00:00:00 will be double counted as existing in both quarters
2) similarly, the information will be duplicately visualized when grouping by custom quarter
So back to square one.
The Idea: For Custom Quarter creation, since we cannot control the date/time, please force the end date of the range to always reflect end of day of the end date as in 23:59:59.