I faced this issue with the prototype model I have been using that if we are going with non-integer aggregation latency, the frame file will have to be named decimal points in the GPS times.
For example, the frame that comes from a kernel ending at 1230000000, the 1s frame that we write after allowing an aggregation latency of 0.25, will be named (under the standard naming strategy followed in LIGO) as something like H-H1_HOFT-1229999998.75-1.gwf
which follows H-H1_HOFT-{start}-{duration}.gwf
Earlier it appeared ugly to me and I kept the timestamps to integers as if we did not apply an aggregation latency while it was actually applied (and terribly forgot about it :( ). This is what eventually led to the inconsistencies in the PE tests as the injected signals were not found at the times they were expected to be.
What is the solution in the long term?