Adding SQL indes causing performance degradation?

Does anyone have experience with existing applications slowing down after
adding 1 or more SQL indexes to a physical file used by the application?

Here are the details.

Our nightly payment processing writes each received payment to a historical
transaction physical file.  This file contains 89+ million records.  In
January we created three SQL indexes over this file to improve query
processes.  Evaluating the run times compared to transaction volume shows a
significant spike in run time without an increase in transaction volume
around the time these indexes were created.  The job is consistently running
about 20 minutes longer than before the indexes were created.

Friday we removed all but one index that is part of other production
applications.  The run time did not improve.  

The SQL index is being pointed to as the reason for the longer run time.  I
can't come up with a reason this would be either true or false.  It seems to
me it wouldn't impact performance any more than adding another DDS created
logical. 

The statement used to create the index is:
 create index lnp00701s4 on lnp00701 (lhtc1)

Anyone have any ideas?

Rick