The Virtuoso isql command output is showing the query execution time in the Virtuoso engine, whereas you timing from the command line would also include the OS time for processing the query and displaying the result.

You can also use the OS time function to time the queries running time in the terminal session which breaks the time down into real, user & system times:

De-iMac-2692:~ hwilliams$ time isql 1111 dba dba exec="sparql select * where {?s ?p ?o} limit 1;"
Connected to OpenLink Virtuoso
Driver: 07.20.3214 OpenLink Virtuoso ODBC Driver
OpenLink Interactive SQL (Virtuoso), version 0.9849b.
Type HELP; for help and EXIT; to exit.
s                                                                                 p                                                                                 o
LONG VARCHAR                                                                      LONG VARCHAR                                                                      LONG VARCHAR
_______________________________________________________________________________

http://www.w3.org/1999/02/22-rdf-syntax-ns#type                                   http://www.w3.org/1999/02/22-rdf-syntax-ns#type                                   http://www.w3.org/1999/02/22-rdf-syntax-ns#Property

1 Rows. -- 0 msec.

real	0m0.006s
user	0m0.002s
sys	0m0.002s
De-iMac-2692:~ hwilliams$

Note the Virtuoso profile function can provide the query compilation and execution times in the Virtuoso engine as detailed in the How can I get full explain and profile plans for a simple SPARQL query documentation.