Use GROUP BY

    SELECT t1.id AS id1, t2.id AS id2, 
    Min(Distance(t1.GEOMETRY,t2.GEOMETRY)) AS DIST 
    FROM fdo_fc1 AS t1, fdo_fc2 AS t2
    GROUP BY t1.id
    ORDER BY id1;

    
Result with my test data:

    id1	id2	DIST
    1	3	16.278821
    2	2	35.114100
    3	1	44.721360
    4	15	65.734314
    5	14	43.289722
    6	1	68.029405
    7	22	56.727418
    8	13	48.301139
    9	10	60.876925
    10	4	34.205263
    11	9	51.224994
    12	10	54.817880
    13	10	47.853944
    14	9	64.124878
    15	8	39.560081
    16	7	59.304300
    17	4	62.169124


I don't understand why your latter query gives only 1x32 results (you have 32 records in the second test table instead of 23, haven't you?). For me it returns the full distance matrix 17x23=391 rows. I made my test tables as you describes with 17 and 23 rows.