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Motifs doesn't find a known motif in my protein.

Motifs looks for sequence motifs by searching through proteins for the patterns defined in the PROSITE Dictionary of Protein Sites and Patterns. Could your 'known motif' be a frequent motif, one that is seen commonly in protein sequences? By default, the program does not show these in its output. You need to use the '-frequent' option for the 'motifs' program to pick out common motifs such as leucine zippers.

From the GCG help on motifs: 

 The PROSITE Dictionary  contains  a number of short sequence patterns
 that occur frequently in protein sequences.  Most of these frequently
 found  patterns  are  post-translational  modifications,   but   more
 specific  patterns  such  as  leucine  zippers  also  fall  into this
 category.  Such frequently  found patterns are  not normally shown by
 Motifs,  but you can display them  by  using the command-line  option
 -FREquent.   More  so  than  with  other   patterns  in  the  PROSITE
 Dictionary,  the presence of these frequently occurring patterns does
 not assure  you that the  protein actually contains the corresponding
 function.

 Here are the patterns that the PROSITE Dictionary classifies
 as frequently occurring in Release 14.0:
 
;Amidation            1 xG(R,K)(R,K)                                 0009.pdoc
;Asn_Glycosylation    1 N~(P)(S,T)~(P)                               0001.pdoc
;Camp_Phospho_Site    1 (R,K)2x(S,T)                                 0004.pdoc
;Ck2_Phospho_Site     1 (S,T)x2(D,E)                                 0006.pdoc
;Glycosaminoglycan    1 SGxG                                         0002.pdoc
;Leucine_Zipper       1 Lx6Lx6Lx6L                                   0029.pdoc
;Microbodies_Cter     1 (S,T,A,G,C,N)(R,K,H)(L,I,V,M,A,F,Y)>         0299.pdoc
;Myristyl             1 G~(E,D,R,K,H,P,F,Y,W)x2(S,T,A,G,C,N)~(P)     0008.pdoc
;Pkc_Phospho_Site     1 (S,T)x(R,K)                                  0005.pdoc
;Rgd                  1 RGD                                          0016.pdoc
;Tyr_Phospho_Site     1 (R,K)x{2,3}(D,E)x{2,3}Y                      0007.pdoc